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[ { "id": "949336__text", "type": "abstract", "text": [ "Hydroxylation of lysine and glycosylation of hydroxylysine during collagen biosynthesis in isolated chick-embryo cartilage cells. \nHydroxylation of lysine and glycosylation of hydroxylysine during collagen biosynthesis in isolated chick-embryo cartilage cells were studied by using continuous labelling and pulse-chase labelling experiments with [14C]lysine. Control experiments with [14C]proline indicated that in continuous labelling the hydroxylation of [14C]proline became linear with time after about 4 min and the secretion of collagen after about 35 min, as reported previously. In similar experiments with [14C]lysine the hydroxylation of [14C]lysine and the glycosylations of hydroxy[14C]lysine became linear at about 4 min, suggesting that these reactions were initiated while the polypeptide chains were growing on the ribosomes. Pulse-chase labelling experiments with [14C]lysine indicated that after a 5 min pulse-label the hydroxylation of [14C]lysine and the glycosylations of hydroxyl[14C]lysine continued during the chase period for about 20 min. The data suggest that these reactions are continued after the release of complete polypeptide chains into the cisternae of the endoplasmic reticulum, whereas the reactions are probably not continued after the formation of the triple helix and the movement of the molecules into the Golgi vacuoles. " ], "offsets": [ [ 0, 1362 ] ] } ]

[ { "id": "949336_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 66, 74 ] ], "normalized": [] }, { "id": "949336_T2", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 197, 205 ] ], "normalized": [] }, { "id": "949336_T3", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 533, 541 ] ], "normalized": [] }, { "id": "949336_T5", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 17, 23 ] ], "normalized": [] }, { "id": "949336_T7", "type": "Entity", "text": [ "hydroxylysine" ], "offsets": [ [ 45, 58 ] ], "normalized": [] }, { "id": "949336_T9", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 148, 154 ] ], "normalized": [] }, { "id": "949336_T11", "type": "Entity", "text": [ "hydroxylysine" ], "offsets": [ [ 176, 189 ] ], "normalized": [] }, { "id": "949336_T13", "type": "Entity", "text": [ "[14C]proline" ], "offsets": [ [ 457, 469 ] ], "normalized": [] }, { "id": "949336_T15", "type": "Entity", "text": [ "[14C]lysine" ], "offsets": [ [ 647, 658 ] ], "normalized": [] }, { "id": "949336_T17", "type": "Entity", "text": [ "hydroxy[14C]lysine" ], "offsets": [ [ 685, 703 ] ], "normalized": [] }, { "id": "949336_T19", "type": "Entity", "text": [ "[14C]lysine" ], "offsets": [ [ 954, 965 ] ], "normalized": [] }, { "id": "949336_T21", "type": "Entity", "text": [ "hydroxyl[14C]lysine" ], "offsets": [ [ 992, 1011 ] ], "normalized": [] } ]

[ { "id": "949336_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "Hydroxylation" ], "offsets": [ [ 0, 13 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T1" }, { "role": "Site", "ref_id": "949336_T5" } ] }, { "id": "949336_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 28, 41 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T1" }, { "role": "Site", "ref_id": "949336_T7" } ] }, { "id": "949336_E3", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "Hydroxylation" ], "offsets": [ [ 131, 144 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T2" }, { "role": "Site", "ref_id": "949336_T9" } ] }, { "id": "949336_E4", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 159, 172 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T2" }, { "role": "Site", "ref_id": "949336_T11" } ] }, { "id": "949336_E5", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 440, 453 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T3" }, { "role": "Site", "ref_id": "949336_T13" } ] }, { "id": "949336_E6", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 630, 643 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T3" }, { "role": "Site", "ref_id": "949336_T15" } ] }, { "id": "949336_E7", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylations" ], "offsets": [ [ 667, 681 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T3" }, { "role": "Site", "ref_id": "949336_T17" } ] }, { "id": "949336_E8", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 937, 950 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T3" }, { "role": "Site", "ref_id": "949336_T19" } ] }, { "id": "949336_E9", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylations" ], "offsets": [ [ 974, 988 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "949336_T3" }, { "role": "Site", "ref_id": "949336_T21" } ] } ]

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[ { "id": "1935961__text", "type": "abstract", "text": [ "Tricholongins BI and BII, 19-residue peptaibols from Trichoderma longibrachiatum. Solution structure from two-dimensional NMR spectroscopy. \nTwo nonadecapeptides, tricholongins BI and BII, which display antifungal and antibacterial activities, have been isolated from in vitro cultures of the fungus Trichoderma longibrachiatum. The peptides were separated by reversed-phase HPLC; their amino acid compositions were determined by gas chromatography and their sequences by positive-ion fast-atom-bombardment mass spectrometry and high-field NMR. These linear peptides, containing mainly hydrophobic L-amino acids, 8-9 2-aminoisobutyric acid residues and exhibiting an acetylated N-terminal residue and an amino alcohol C-terminal leucinol belong to the peptaibol class. The methanol solution structure of tricholongins BI and BII has been investigated using both one- and two-dimensional NMR techniques. The total 1H-NMR and 13C-NMR assignments are given. By a combination of the 3JNH,C alpha H coupling constant values, temperature coefficients of the NH and CO groups, amide hydrogen/deuterium-exchange rate measurements and NOE data, a secondary structure for tricholongins in solution has been proposed. Both peptides adopt a similar alpha-helical conformation with a hinge around Pro13 resulting from two 3(10) bonds. The results suggest that the N-terminus contains mixed alpha/3(10) bonds. The membrane permeability modifications induced by tricholongins have been assayed by the use of liposomes composed of egg phosphatidylcholine with 20-30% cholesterol. The peptide-induced leakage of an entrapped fluorescent probe has been followed by fluorescence spectroscopy. In a concentration range of 0.13-0.31 microM, tricholongins induce the leakage of 50% of the entrapped material in 20 min. " ], "offsets": [ [ 0, 1797 ] ] } ]

[ { "id": "1935961_T1", "type": "Protein", "text": [ "Tricholongins BI" ], "offsets": [ [ 0, 16 ] ], "normalized": [] }, { "id": "1935961_T2", "type": "Protein", "text": [ "BII" ], "offsets": [ [ 21, 24 ] ], "normalized": [] }, { "id": "1935961_T3", "type": "Protein", "text": [ "tricholongins BI" ], "offsets": [ [ 163, 179 ] ], "normalized": [] }, { "id": "1935961_T4", "type": "Protein", "text": [ "BII" ], "offsets": [ [ 184, 187 ] ], "normalized": [] }, { "id": "1935961_T5", "type": "Protein", "text": [ "tricholongins BI" ], "offsets": [ [ 804, 820 ] ], "normalized": [] }, { "id": "1935961_T6", "type": "Protein", "text": [ "BII" ], "offsets": [ [ 825, 828 ] ], "normalized": [] }, { "id": "1935961_T8", "type": "Entity", "text": [ "N-terminal residue" ], "offsets": [ [ 678, 696 ] ], "normalized": [] } ]

[ { "id": "1935961_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 667, 677 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1935961_T3" }, { "role": "Site", "ref_id": "1935961_T8" } ] }, { "id": "1935961_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 667, 677 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1935961_T4" }, { "role": "Site", "ref_id": "1935961_T8" } ] } ]

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[ { "id": "7356670__text", "type": "abstract", "text": [ "The complete amino acid sequence of the Ca2+-dependent modulator protein (calmodulin) of bovine brain. \nWe present the data required to establish the complete amino acid sequence of bovine brain modulator protein, the multifunctional calcium-dependent regulatory protein. Bovine brain modulator protein contains 148 amino acid residues and has a molecular mass of 16,680 daltons. The protein commences with an acetylated alanyl residue in accord with the previous report that its NH2 terminus was blocked. The single residues of histidine and trimethyllysine occur at positions 107 and 115, respectively, in a region of the linear sequence implicated by other studies as important for calcium-dependent modulator protein-enzyme interactions. The sequence of bovine brain modulator protein demonstrated here is closely related to those of muscle troponin Cs, as originally suggested from considerations of the similarities in calcium binding and functional and physicochemical properties of these proteins (Watterson, D.M., Harrelson, W.G., Jr., Keller, P.M., Sharief, F., and Vanaman, T.C. (1976) J. Biol. chem. 251, 4501-4513). The linear amino acid sequence of bovine brain modulator protein is composed of four internally homologous sequences or domains, each of which contains the appropriate amino acids arranged so as to form a helix-loop-helix, calcium-binding structure. The high level of internal homology of bovine brain modulator protein and its relationship to the other members of the calcium-binding protein superfamily provide convincing evidence that 1) it arose early in the evolution of these related proteins and 2) it was formed by two successive tandem duplications of a gene encoding a small, single domain ancestral precursor. Comparison with the nearly complete sequences of the bovine uterus and rat testis modulator proteins reported by other laboratories indicates that this ubiquitous calcium-dependent regulatory protein does not occur in tissue-specific forms, commensurate with the proposed function of modulator protein as a mediator of calcium-second messenger function in eukaryotic cells. " ], "offsets": [ [ 0, 2124 ] ] } ]

[ { "id": "7356670_T1", "type": "Protein", "text": [ "Ca2+-dependent modulator protein" ], "offsets": [ [ 40, 72 ] ], "normalized": [] }, { "id": "7356670_T2", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 74, 84 ] ], "normalized": [] }, { "id": "7356670_T4", "type": "Entity", "text": [ "alanyl residue" ], "offsets": [ [ 421, 435 ] ], "normalized": [] } ]

[ { "id": "7356670_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 410, 420 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7356670_T2" }, { "role": "Site", "ref_id": "7356670_T4" } ] } ]

[ { "id": "7356670_1", "entity_ids": [ "7356670_T1", "7356670_T2" ] } ]

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[ { "id": "3049594__text", "type": "abstract", "text": [ "Bovine factor VII. Its purification and complete amino acid sequence. \nA modified method for purification of blood clotting factor VII from bovine plasma was developed, and its complete amino acid sequence was established. The isolated factor VII was activated with factor XIIa, and the resulting two-chain factor VII (factor VIIa) was reduced and S-pyridylethylated or S-aminoethylated. The amino acid sequences of the S-alkylated heavy and light chains were determined by sequencing the fragments obtained from enzymatic and chemical cleavages. Fast atom bombardment mass spectrometry was also used to establish the COOH-terminal sequence of the heavy chain. The light chain consists of 152 residues with one carbohydrate chain at Asn145, and 11 gamma-carboxyglutamic acid residues are found within the NH2-terminal 35 residues. The light chain contains 0.2-0.3 mol of beta-hydroxyaspartic acid/mol of protein, indicating that an aspartic acid residue in bovine factor VII is incompletely hydroxylated. Moreover, a pentapeptide, Ala-Ser*-Ser-Pro-Cys (positions 51-55), isolated from an enzymatic digest of the light chain, contained an unknown serine derivative, but its structure is still unclear. On the other hand, the heavy chain is composed of 255 residues and one asparagine-linked carbohydrate chain at Asn203. Bovine factor VII, with a total of 407 residues, has 71% sequence identity with the human molecule (406 residues) predicted from the cDNA sequence (Hagen, F. S., Gray, C. L., O'Hara, P., Grant, F. J., Saari, G. C., Woodbury, R. G., Hart, C. E., Insley, M., Kisiel, W., Kurachi, K., and Davie, E. W. (1986) Proc. Natl. Acad. Sci. U. S. A. 83, 2412-2416). " ], "offsets": [ [ 0, 1681 ] ] } ]

[ { "id": "3049594_T1", "type": "Protein", "text": [ "factor VII" ], "offsets": [ [ 7, 17 ] ], "normalized": [] }, { "id": "3049594_T2", "type": "Protein", "text": [ "factor VII" ], "offsets": [ [ 124, 134 ] ], "normalized": [] }, { "id": "3049594_T3", "type": "Protein", "text": [ "factor VII" ], "offsets": [ [ 237, 247 ] ], "normalized": [] }, { "id": "3049594_T4", "type": "Protein", "text": [ "factor XIIa" ], "offsets": [ [ 267, 278 ] ], "normalized": [] }, { "id": "3049594_T5", "type": "Protein", "text": [ "factor VII" ], "offsets": [ [ 308, 318 ] ], "normalized": [] }, { "id": "3049594_T6", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 320, 331 ] ], "normalized": [] }, { "id": "3049594_T7", "type": "Protein", "text": [ "factor VII" ], "offsets": [ [ 969, 979 ] ], "normalized": [] }, { "id": "3049594_T8", "type": "Protein", "text": [ "factor VII" ], "offsets": [ [ 1334, 1344 ] ], "normalized": [] }, { "id": "3049594_T9", "type": "Entity", "text": [ "aspartic acid residue" ], "offsets": [ [ 937, 958 ] ], "normalized": [] }, { "id": "3049594_T10", "type": "Entity", "text": [ "bovine factor VII" ], "offsets": [ [ 962, 979 ] ], "normalized": [] } ]

[ { "id": "3049594_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ " hydroxylate" ], "offsets": [ [ 995, 1007 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3049594_T7" }, { "role": "Site", "ref_id": "3049594_T9" } ] } ]

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[ { "id": "8507662__text", "type": "abstract", "text": [ "Pro-major basic protein has three types of sugar chains at the pro-portion. \nThe amino-acid sequence of purified recombinant pro-major basic protein from Chinese hamster kidney cells was determined to verify the primary structure and glycosylation sites. Reduced and S-carboxamidemethylated protein was first digested with Achromobacter proteinase I. Each peptide was characterized by amino-acid analysis and amino-acid sequence analysis. We could identify all the peptides which were expected from the pro-major basic protein cDNA sequence. Sequence analysis and deglycosylation study revealed that Ser-8, Thr-9, Ser-46 and Asn-70 were glycosylated. The results indicated that proMBP has three types of sugar chains, O-glycoside, N-glycoside and glycosaminoglycan, in the pro-portion. " ], "offsets": [ [ 0, 790 ] ] } ]

[ { "id": "8507662_T1", "type": "Protein", "text": [ "Pro-major basic protein" ], "offsets": [ [ 0, 23 ] ], "normalized": [] }, { "id": "8507662_T2", "type": "Protein", "text": [ "pro-major basic protein" ], "offsets": [ [ 125, 148 ] ], "normalized": [] }, { "id": "8507662_T3", "type": "Protein", "text": [ "proteinase I" ], "offsets": [ [ 338, 350 ] ], "normalized": [] }, { "id": "8507662_T4", "type": "Protein", "text": [ "pro-major basic protein" ], "offsets": [ [ 506, 529 ] ], "normalized": [] }, { "id": "8507662_T5", "type": "Protein", "text": [ "proMBP" ], "offsets": [ [ 682, 688 ] ], "normalized": [] }, { "id": "8507662_T6", "type": "Entity", "text": [ "pro-major basic protein" ], "offsets": [ [ 506, 529 ] ], "normalized": [] }, { "id": "8507662_T7", "type": "Entity", "text": [ "Ser-8" ], "offsets": [ [ 604, 609 ] ], "normalized": [] }, { "id": "8507662_T8", "type": "Entity", "text": [ "Thr-9" ], "offsets": [ [ 611, 616 ] ], "normalized": [] }, { "id": "8507662_T9", "type": "Entity", "text": [ "Ser-46" ], "offsets": [ [ 618, 624 ] ], "normalized": [] }, { "id": "8507662_T10", "type": "Entity", "text": [ "Asn-70" ], "offsets": [ [ 629, 635 ] ], "normalized": [] } ]

[ { "id": "8507662_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 641, 653 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8507662_T4" }, { "role": "Site", "ref_id": "8507662_T7" } ] }, { "id": "8507662_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 641, 653 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8507662_T4" }, { "role": "Site", "ref_id": "8507662_T10" } ] }, { "id": "8507662_E3", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 641, 653 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8507662_T4" }, { "role": "Site", "ref_id": "8507662_T9" } ] }, { "id": "8507662_E4", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 641, 653 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8507662_T4" }, { "role": "Site", "ref_id": "8507662_T8" } ] } ]

[ { "id": "8507662_1", "entity_ids": [ "8507662_T4", "8507662_T4" ] } ]

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[ { "id": "1339288__text", "type": "abstract", "text": [ "Comparison of cobalamin-independent and cobalamin-dependent methionine synthases from Escherichia coli: two solutions to the same chemical problem. \nIn Escherichia coli, two enzymes catalyze the synthesis of methionine from homocysteine using methyltetrahydrofolate as the donor of the required methyl group: cobalamin-dependent and cobalamin-independent methionine synthases. Comparison of the mechanisms of these two enzymes offers the opportunity to examine two different solutions to the same chemical problem. We initiated the research described here to determine whether the two enzymes were evolutionarily related by comparing the deduced amino acid sequences of the two proteins. We have determined the nucleotide sequence for the metE gene, encoding the cobalamin-independent methionine synthase. Our results reveal an absence of similarity between the deduced amino acid sequences of the cobalamin-dependent and cobalamin-independent proteins and suggest that the two have arisen by convergent evolution. We have developed a rapid one-step purification of the recombinant cobalamin-independent methionine synthase (MetE) that yields homogeneous protein in high yield for mechanistic and structural studies. In the course of these studies, we identified a highly reactive thiol in MetE that is alkylated by chloromethyl ketones and by iodoacetamide. We demonstrated that alkylation of this residue, shown to be cysteine 726, results in complete loss of activity. While we are unable to deduce the role of cysteine 726 in catalysis at this time, the identification of this reactive residue suggests the possibility that this thiol functions as an intermediate methyl acceptor in catalysis, analogous to the role of cobalamin in the reaction catalyzed by the cobalamin-dependent enzyme. " ], "offsets": [ [ 0, 1802 ] ] } ]

[ { "id": "1339288_T1", "type": "Protein", "text": [ "metE" ], "offsets": [ [ 742, 746 ] ], "normalized": [] }, { "id": "1339288_T2", "type": "Protein", "text": [ "cobalamin-independent methionine synthase" ], "offsets": [ [ 1087, 1128 ] ], "normalized": [] }, { "id": "1339288_T3", "type": "Protein", "text": [ "MetE" ], "offsets": [ [ 1130, 1134 ] ], "normalized": [] }, { "id": "1339288_T4", "type": "Protein", "text": [ "MetE" ], "offsets": [ [ 1296, 1300 ] ], "normalized": [] }, { "id": "1339288_T5", "type": "Entity", "text": [ "cysteine 726" ], "offsets": [ [ 1522, 1534 ] ], "normalized": [] }, { "id": "1339288_T7", "type": "Entity", "text": [ "cobalamin-dependent enzyme" ], "offsets": [ [ 1774, 1800 ] ], "normalized": [] } ]

[ { "id": "1339288_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ " catalyze" ], "offsets": [ [ 1756, 1765 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1339288_T4" }, { "role": "Cause", "ref_id": "1339288_T7" }, { "role": "Site", "ref_id": "1339288_T5" } ] } ]

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[ { "id": "17511883__text", "type": "abstract", "text": [ "The non-dosage compensated Lsp1alpha gene of Drosophila melanogaster escapes acetylation by MOF in larval fat body nuclei, but is flanked by two dosage compensated genes. \nBACKGROUND: In Drosophila melanogaster dosage compensation of most X-linked genes is mediated by the male-specific lethal (MSL) complex, which includes MOF. MOF acetylates histone H4 at lysine 16 (H4K16ac). The X-linked Larval serum protein one alpha (Lsp1alpha) gene has long been known to be not dosage compensated. Here we have examined possible explanations for why the Lsp1alpha gene is not dosage compensated. RESULTS: Quantitative RNase protection analysis showed that the genes flanking Lsp1alpha are expressed equally in males and females and confirmed that Lsp1alpha is not dosage compensated. Unlike control X-linked genes, Lsp1alpha was not enriched for H4K16ac in the third instar larval fat body, the tissue in which the gene is actively expressed. X-linked Lsp1alpha promoter-lacZ reporter transgenes are enriched for H4K16ac in third instar larval fat body. An X-linked reporter gene bracketed by Lsp1alpha flanking regions was dosage compensated. One of the genes flanking Lsp1alpha is expressed in the same tissue. This gene shows a modest enrichment for H4K16ac but only at the part of the gene most distant from Lsp1alpha. Phylogenetic analyses of the sequences of the genomes of 12 Drosophila species shows that Lsp1alpha is only present within the melanogaster subgroup of species. CONCLUSION: Lsp1alpha is not modified by the MSL complex but is in a region of the X chromosome that is regulated by the MSL complex. The high activity or tissue-specificity of the Lsp1alpha promoter does not prevent regulation by the MSL complex. The regions flanking Lsp1alpha do not appear to block access by the MSL complex. Lsp1alpha appears to have recently evolved within the melanogaster subgroup of Drosophila species. The most likely explanation for why Lsp1alpha is not dosage compensated is that the gene has not evolved a mechanism to independently recruit the MSL complex, possibly because of its recent evolutionary origin, and because there appears to be a low level of bound MSL complex in a nearby gene that is active in the same tissue. " ], "offsets": [ [ 0, 2232 ] ] } ]

[ { "id": "17511883_T1", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 27, 36 ] ], "normalized": [] }, { "id": "17511883_T2", "type": "Protein", "text": [ "MOF" ], "offsets": [ [ 92, 95 ] ], "normalized": [] }, { "id": "17511883_T3", "type": "Protein", "text": [ "MOF" ], "offsets": [ [ 324, 327 ] ], "normalized": [] }, { "id": "17511883_T4", "type": "Protein", "text": [ "MOF" ], "offsets": [ [ 329, 332 ] ], "normalized": [] }, { "id": "17511883_T5", "type": "Protein", "text": [ "histone H4" ], "offsets": [ [ 344, 354 ] ], "normalized": [] }, { "id": "17511883_T6", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 369, 371 ] ], "normalized": [] }, { "id": "17511883_T7", "type": "Protein", "text": [ "Larval serum protein one alpha" ], "offsets": [ [ 392, 422 ] ], "normalized": [] }, { "id": "17511883_T8", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 424, 433 ] ], "normalized": [] }, { "id": "17511883_T9", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 546, 555 ] ], "normalized": [] }, { "id": "17511883_T10", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 667, 676 ] ], "normalized": [] }, { "id": "17511883_T11", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 739, 748 ] ], "normalized": [] }, { "id": "17511883_T12", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 807, 816 ] ], "normalized": [] }, { "id": "17511883_T13", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 838, 840 ] ], "normalized": [] }, { "id": "17511883_T14", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 944, 953 ] ], "normalized": [] }, { "id": "17511883_T15", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1005, 1007 ] ], "normalized": [] }, { "id": "17511883_T16", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 1085, 1094 ] ], "normalized": [] }, { "id": "17511883_T17", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 1162, 1171 ] ], "normalized": [] }, { "id": "17511883_T18", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1245, 1247 ] ], "normalized": [] }, { "id": "17511883_T19", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 1304, 1313 ] ], "normalized": [] }, { "id": "17511883_T20", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 1405, 1414 ] ], "normalized": [] }, { "id": "17511883_T21", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 1488, 1497 ] ], "normalized": [] }, { "id": "17511883_T22", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 1745, 1754 ] ], "normalized": [] }, { "id": "17511883_T23", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 1805, 1814 ] ], "normalized": [] }, { "id": "17511883_T24", "type": "Protein", "text": [ "Lsp1alpha" ], "offsets": [ [ 1940, 1949 ] ], "normalized": [] }, { "id": "17511883_T27", "type": "Entity", "text": [ "lysine 16" ], "offsets": [ [ 358, 367 ] ], "normalized": [] } ]

[ { "id": "17511883_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylates" ], "offsets": [ [ 333, 343 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "17511883_T5" }, { "role": "Site", "ref_id": "17511883_T27" } ] }, { "id": "17511883_E2", "type": "Positive_regulation", "trigger": { "text": [ "acetylates" ], "offsets": [ [ 333, 343 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "17511883_E1" }, { "role": "Cause", "ref_id": "17511883_T4" } ] } ]

[ { "id": "17511883_1", "entity_ids": [ "17511883_T5", "17511883_T6" ] } ]

[]

[ { "id": "3597352__text", "type": "abstract", "text": [ "Complete amino acid sequence of 14 kDa beta-galactoside-binding lectin of chick embryo. \nThe complete amino acid sequence of a soluble beta-galactoside-binding lectin (subunit MW 14,500) of chick embryo was determined. The protein consists of 134 amino acids beginning with serine and ending with glutamic acid, and its N-terminal was blocked with acetate. The agreement of the present result with that obtained from nucleotide sequence analysis (Y. Ohyama et al. (1986) Biochem. Biophys. Res. Commun. 134, 51-56) indicates the lack of a cleavable leader sequence. Internal homologies were observed in several regions along the polypeptide chain. The highest homology (55% identity) was found between residues 42-58 and residues 112-128. This suggests that chick 14 kDa lectin may have evolved via several gene duplications. " ], "offsets": [ [ 0, 825 ] ] } ]

[ { "id": "3597352_T1", "type": "Protein", "text": [ "beta-galactoside-binding lectin" ], "offsets": [ [ 39, 70 ] ], "normalized": [] }, { "id": "3597352_T2", "type": "Protein", "text": [ "beta-galactoside-binding lectin" ], "offsets": [ [ 135, 166 ] ], "normalized": [] }, { "id": "3597352_T3", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 770, 776 ] ], "normalized": [] }, { "id": "3597352_T4", "type": "Entity", "text": [ "N-terminal" ], "offsets": [ [ 320, 330 ] ], "normalized": [] } ]

[ { "id": "3597352_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked with acetate" ], "offsets": [ [ 335, 355 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3597352_T2" }, { "role": "Site", "ref_id": "3597352_T4" } ] } ]

[ { "id": "3597352_1", "entity_ids": [ "3597352_T2", "3597352_T2" ] } ]

[]

[ { "id": "6248536__text", "type": "abstract", "text": [ "The complete amino acid sequence of horse muscle acylphosphatase. \nThe amino acid sequence of horse muscle acylphosphatase is given in the present paper. The carboxymethylated enzyme consists of a single polypeptide chain of 98 amino acid residues with an acetyl group blocking the NH2 terminus and a tyrosine at the COOH terminus. The calculated molecular weight of the native protein, a mixed disulfide with glutathione, is 11,365. The carboxymethylated protein was cleaved by cyanogen bromide. The three expected fragments were purified; moreover, an additional fragment, derived from a partial failure of cleavage at methionine-24, was purified and characterized. The structures of the cyanogen bromide fragments were established by subfragmentation with endopeptidases, and the sequences of the overlapping subfragments were determined. From the results, it was possible to order the peptides within the sequence and then to establish the complete primary structure of the enzyme. " ], "offsets": [ [ 0, 986 ] ] } ]

[ { "id": "6248536_T1", "type": "Protein", "text": [ "acylphosphatase" ], "offsets": [ [ 49, 64 ] ], "normalized": [] }, { "id": "6248536_T2", "type": "Protein", "text": [ "acylphosphatase" ], "offsets": [ [ 107, 122 ] ], "normalized": [] }, { "id": "6248536_T4", "type": "Entity", "text": [ "NH2 terminus" ], "offsets": [ [ 282, 294 ] ], "normalized": [] }, { "id": "6248536_T5", "type": "Entity", "text": [ "tyrosine" ], "offsets": [ [ 301, 309 ] ], "normalized": [] } ]

[ { "id": "6248536_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetyl group blocking" ], "offsets": [ [ 256, 277 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6248536_T2" }, { "role": "Site", "ref_id": "6248536_T4" } ] }, { "id": "6248536_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetyl group blocking" ], "offsets": [ [ 256, 277 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6248536_T2" }, { "role": "Site", "ref_id": "6248536_T5" } ] } ]

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[]

[ { "id": "497176__text", "type": "abstract", "text": [ "Primary structure of rabbit alpha-lactalbumin. \nRabbit alpha-lactalbumin was purified from the milk of New Zealand White rabbits. It was found to exist predominantly as a glycoprotein, containing 5 mol of glucosamine per mol of protein, as well as other sugars. The amino acid sequence of the protein was determined by sequenator analysis and carboxypeptidase digestion. There are 122 amino acids in the protein and a single carbohydrate moiety, probably attached to an asparagine residue at position 45. The C terminus of rabbit alpha-lactalbumin is one residue shorter than that of the other alpha-lactalbumins. Sequence comparisons indicate that the alpha-lactalbumin gene has been undergoing more frequent mutation than had previously been thought. A new method of preparative peptide mapping using 2,5-diphenyloxazole (PPO) fluor to detect peptides is described. " ], "offsets": [ [ 0, 868 ] ] } ]

[ { "id": "497176_T1", "type": "Protein", "text": [ " alpha-lactalbumin" ], "offsets": [ [ 27, 45 ] ], "normalized": [] }, { "id": "497176_T2", "type": "Protein", "text": [ "alpha-lactalbumin" ], "offsets": [ [ 55, 72 ] ], "normalized": [] }, { "id": "497176_T3", "type": "Protein", "text": [ "alpha-lactalbumin" ], "offsets": [ [ 530, 547 ] ], "normalized": [] }, { "id": "497176_T4", "type": "Protein", "text": [ "alpha-lactalbumin" ], "offsets": [ [ 653, 670 ] ], "normalized": [] }, { "id": "497176_T6", "type": "Entity", "text": [ "asparagine" ], "offsets": [ [ 470, 480 ] ], "normalized": [] } ]

[ { "id": "497176_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate moiety, probably attached" ], "offsets": [ [ 425, 463 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "497176_T2" }, { "role": "Site", "ref_id": "497176_T6" } ] } ]

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[ { "id": "1317796__text", "type": "abstract", "text": [ "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3) from sheep brain. Amino acid sequence of phosphorylated forms. \nA potent inhibitor of protein kinase C (PKC), inhibitor protein-1 (KCIP-1), isolated from sheep brain has been shown to consist of eight isoforms by reverse-phase HPLC. Direct protein sequence analysis has revealed these to be the same as those of 14-3-3 protein, described as an activator of tyrosine and tryptophan hydroxylases involved in neurotransmitter biosynthesis. The N-termini of KCIP-1 isoforms were shown to be acetylated, and secondary structure predictions revealed a high degree of alpha-helix with an amphipathic nature. KCIP-1 showed no inhibitory activity towards protein kinase M (the catalytic fragment of PKC) and had no effect on the activities of three other protein kinases, cAMP-dependent protein kinase, Ca2+/calmodulin-dependent protein kinase II and casein kinase 2. Four forms of KCIP-1 were shown to be substrates for PKC in vitro, but none were phosphorylated by the other protein kinases mentioned above. " ], "offsets": [ [ 0, 1067 ] ] } ]

[ { "id": "1317796_T1", "type": "Protein", "text": [ "protein kinase C inhibitor" ], "offsets": [ [ 23, 49 ] ], "normalized": [] }, { "id": "1317796_T2", "type": "Protein", "text": [ "KCIP-1" ], "offsets": [ [ 51, 57 ] ], "normalized": [] }, { "id": "1317796_T3", "type": "Protein", "text": [ "14-3-3" ], "offsets": [ [ 58, 64 ] ], "normalized": [] }, { "id": "1317796_T4", "type": "Protein", "text": [ "protein kinase C" ], "offsets": [ [ 152, 168 ] ], "normalized": [] }, { "id": "1317796_T5", "type": "Protein", "text": [ "PKC" ], "offsets": [ [ 170, 173 ] ], "normalized": [] }, { "id": "1317796_T6", "type": "Protein", "text": [ "inhibitor protein-1" ], "offsets": [ [ 176, 195 ] ], "normalized": [] }, { "id": "1317796_T7", "type": "Protein", "text": [ "KCIP-1" ], "offsets": [ [ 197, 203 ] ], "normalized": [] }, { "id": "1317796_T8", "type": "Protein", "text": [ "14-3-3" ], "offsets": [ [ 378, 384 ] ], "normalized": [] }, { "id": "1317796_T9", "type": "Protein", "text": [ "KCIP-1" ], "offsets": [ [ 520, 526 ] ], "normalized": [] }, { "id": "1317796_T10", "type": "Protein", "text": [ "KCIP-1" ], "offsets": [ [ 667, 673 ] ], "normalized": [] }, { "id": "1317796_T11", "type": "Protein", "text": [ "PKC" ], "offsets": [ [ 756, 759 ] ], "normalized": [] }, { "id": "1317796_T12", "type": "Protein", "text": [ "KCIP-1" ], "offsets": [ [ 939, 945 ] ], "normalized": [] }, { "id": "1317796_T13", "type": "Protein", "text": [ "PKC" ], "offsets": [ [ 978, 981 ] ], "normalized": [] }, { "id": "1317796_T14", "type": "Entity", "text": [ "N-termini" ], "offsets": [ [ 507, 516 ] ], "normalized": [] } ]

[ { "id": "1317796_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 553, 563 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1317796_T9" }, { "role": "Site", "ref_id": "1317796_T14" } ] } ]

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[ { "id": "3525533__text", "type": "abstract", "text": [ "Complete amino acid sequences of bovine and human endozepines. Homology with rat diazepam binding inhibitor. \nThe complete amino acid sequences of bovine and human brain endozepines have been determined. The amino-terminal serine of both endozepines is acylated. Assignment of the first 7 residues was achieved through Edman degradation after acid-induced rearrangement and subsequent acid hydrolysis of the amino-terminal blocking group. Cleavage of endozepine by chemical and enzymatic techniques established all the fragments in an unambiguous sequence. Bovine and human endozepines are single-chain polypeptides of 86 residues, with calculated molecular weights of 9913, displaying 93% homology. A comparison between the sequences of bovine and human endozepines with the partial sequences of the functionally related diazepam binding inhibitor from rat brain reveals significant sequence homology. The reported results suggest that bovine and human endozepines as well as rat diazepam binding inhibitor belong to a new family of polypeptides which presumably take part in the modulation of gamma-aminobutyric acid-ergic transmission. " ], "offsets": [ [ 0, 1139 ] ] } ]

[ { "id": "3525533_T1", "type": "Protein", "text": [ "endozepines" ], "offsets": [ [ 50, 61 ] ], "normalized": [] }, { "id": "3525533_T2", "type": "Protein", "text": [ "endozepines" ], "offsets": [ [ 170, 181 ] ], "normalized": [] }, { "id": "3525533_T3", "type": "Protein", "text": [ "endozepines" ], "offsets": [ [ 238, 249 ] ], "normalized": [] }, { "id": "3525533_T4", "type": "Protein", "text": [ "endozepine" ], "offsets": [ [ 451, 461 ] ], "normalized": [] }, { "id": "3525533_T5", "type": "Protein", "text": [ "endozepines" ], "offsets": [ [ 574, 585 ] ], "normalized": [] }, { "id": "3525533_T6", "type": "Protein", "text": [ "endozepines" ], "offsets": [ [ 755, 766 ] ], "normalized": [] }, { "id": "3525533_T7", "type": "Protein", "text": [ "endozepines" ], "offsets": [ [ 954, 965 ] ], "normalized": [] }, { "id": "3525533_T8", "type": "Entity", "text": [ "serine" ], "offsets": [ [ 223, 229 ] ], "normalized": [] } ]

[ { "id": "3525533_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acylated" ], "offsets": [ [ 253, 261 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3525533_T3" }, { "role": "Site", "ref_id": "3525533_T8" } ] } ]

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[ { "id": "8615697__text", "type": "abstract", "text": [ "Glycosylation in human thyroglobulin: location of the N-linked oligosaccharide units and comparison with bovine thyroglobulin. \nThe amino acid sequence established for human thyroglobulin (hTG) from its cDNA sequence contains 20 putative N-linked glycosylation sites. We have characterized the glycopeptides contained in a tryptic digest of hTG in order to determine which sites are actually linked to carbohydrate. In addition, the distribution of oligosaccharide type(s) at these confirmed sites of N-linked glycosylation has been examined. Glycopeptides were purified using gel permeation chromatography followed by several steps of HPLC. The purified tryptic glycopeptides were characterized by gas phase sequencing and carbohydrate analysis and located within the amino acid sequence of thyroglobulin. Each of the recovered glycopeptides contained a consensus sequence for N-linked glycosylation. Of the 20 putative N-linked glycosylation sites in the human thyroglobulin polypeptide chain, 16 were shown to be actually glycosylated in the mature protein. Eight of these confirmed glycosylation sites (at positions 57, 465, 510, 729, 797, 1696, 1754, and 2230) appear to be linked to complex-type oligosaccharide units containing fucose and galactose in addition to mannose and glucosamine. Five sites (at positions 1200, 1329, 1993, 2275, and 2562) contain high mannose type units and two sites (at positions 179 and 1345) are linked to oligosaccharide units containing galactose in addition to mannose and glucosamine but no fucose and may be either hybrid or complex structures. In addition, position 928 was found to be degenerate in oligosaccharide structure and very different oligosaccharide composition types were found associated with peptides containing the same amino acid sequence. A high probability of a beta turn which would include the glycosylated asparagine residue was predicted for the amino acid sequence found at 13 of the 16 sites. The glycosylation pattern in hTG was also compared with the data recently reported for bovine thyroglobulin (bTG) (27) and as has been recently reported for bTG, no oligosaccharides of the high mannose type were found in the N-terminal portion of hTG. Only four of the 20 putative sites the sequence of hTG, at asparagine residues 91, 477, 1849, and 2102 were not represented in the purified glycopeptide population and are presumed to escape significant glycosylation. " ], "offsets": [ [ 0, 2430 ] ] } ]

[ { "id": "8615697_T1", "type": "Protein", "text": [ "thyroglobulin" ], "offsets": [ [ 23, 36 ] ], "normalized": [] }, { "id": "8615697_T2", "type": "Protein", "text": [ "thyroglobulin" ], "offsets": [ [ 112, 125 ] ], "normalized": [] }, { "id": "8615697_T3", "type": "Protein", "text": [ "thyroglobulin" ], "offsets": [ [ 174, 187 ] ], "normalized": [] }, { "id": "8615697_T4", "type": "Protein", "text": [ "hTG" ], "offsets": [ [ 189, 192 ] ], "normalized": [] }, { "id": "8615697_T5", "type": "Protein", "text": [ "hTG" ], "offsets": [ [ 341, 344 ] ], "normalized": [] }, { "id": "8615697_T6", "type": "Protein", "text": [ "thyroglobulin" ], "offsets": [ [ 792, 805 ] ], "normalized": [] }, { "id": "8615697_T7", "type": "Protein", "text": [ "thyroglobulin" ], "offsets": [ [ 963, 976 ] ], "normalized": [] }, { "id": "8615697_T8", "type": "Protein", "text": [ "hTG" ], "offsets": [ [ 1989, 1992 ] ], "normalized": [] }, { "id": "8615697_T9", "type": "Protein", "text": [ "thyroglobulin" ], "offsets": [ [ 2054, 2067 ] ], "normalized": [] }, { "id": "8615697_T10", "type": "Protein", "text": [ "bTG" ], "offsets": [ [ 2069, 2072 ] ], "normalized": [] }, { "id": "8615697_T11", "type": "Protein", "text": [ "bTG" ], "offsets": [ [ 2117, 2120 ] ], "normalized": [] }, { "id": "8615697_T12", "type": "Protein", "text": [ "hTG" ], "offsets": [ [ 2207, 2210 ] ], "normalized": [] }, { "id": "8615697_T13", "type": "Protein", "text": [ "hTG" ], "offsets": [ [ 2263, 2266 ] ], "normalized": [] }, { "id": "8615697_T15", "type": "Entity", "text": [ "N-linked oligosaccharide" ], "offsets": [ [ 54, 78 ] ], "normalized": [] }, { "id": "8615697_T16", "type": "Entity", "text": [ "N-linked glycosylation sites" ], "offsets": [ [ 921, 949 ] ], "normalized": [] }, { "id": "8615697_T18", "type": "Entity", "text": [ "positions 57" ], "offsets": [ [ 1110, 1122 ] ], "normalized": [] }, { "id": "8615697_T19", "type": "Entity", "text": [ "465" ], "offsets": [ [ 1124, 1127 ] ], "normalized": [] }, { "id": "8615697_T20", "type": "Entity", "text": [ "510" ], "offsets": [ [ 1129, 1132 ] ], "normalized": [] }, { "id": "8615697_T21", "type": "Entity", "text": [ "729" ], "offsets": [ [ 1134, 1137 ] ], "normalized": [] }, { "id": "8615697_T22", "type": "Entity", "text": [ "797" ], "offsets": [ [ 1139, 1142 ] ], "normalized": [] }, { "id": "8615697_T23", "type": "Entity", "text": [ "1696" ], "offsets": [ [ 1144, 1148 ] ], "normalized": [] }, { "id": "8615697_T24", "type": "Entity", "text": [ "1754" ], "offsets": [ [ 1150, 1154 ] ], "normalized": [] }, { "id": "8615697_T25", "type": "Entity", "text": [ "2230" ], "offsets": [ [ 1160, 1164 ] ], "normalized": [] }, { "id": "8615697_T27", "type": "Entity", "text": [ "positions 1200" ], "offsets": [ [ 1311, 1325 ] ], "normalized": [] }, { "id": "8615697_T28", "type": "Entity", "text": [ "1329" ], "offsets": [ [ 1327, 1331 ] ], "normalized": [] }, { "id": "8615697_T29", "type": "Entity", "text": [ "1993" ], "offsets": [ [ 1333, 1337 ] ], "normalized": [] }, { "id": "8615697_T30", "type": "Entity", "text": [ "2275" ], "offsets": [ [ 1339, 1343 ] ], "normalized": [] }, { "id": "8615697_T31", "type": "Entity", "text": [ "2562" ], "offsets": [ [ 1349, 1353 ] ], "normalized": [] }, { "id": "8615697_T33", "type": "Entity", "text": [ "positions 179" ], "offsets": [ [ 1405, 1418 ] ], "normalized": [] }, { "id": "8615697_T34", "type": "Entity", "text": [ "1345" ], "offsets": [ [ 1423, 1427 ] ], "normalized": [] }, { "id": "8615697_T37", "type": "Entity", "text": [ "asparagine residue" ], "offsets": [ [ 1870, 1888 ] ], "normalized": [] } ]

[ { "id": "8615697_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glycosylation" ], "offsets": [ [ 0, 13 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T1" }, { "role": "Site", "ref_id": "8615697_T15" } ] }, { "id": "8615697_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 1025, 1037 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T16" } ] }, { "id": "8615697_E3", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to complex-type oligosaccharide units" ], "offsets": [ [ 1179, 1223 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T24" } ] }, { "id": "8615697_E4", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to complex-type oligosaccharide units" ], "offsets": [ [ 1179, 1223 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T20" } ] }, { "id": "8615697_E5", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to complex-type oligosaccharide units" ], "offsets": [ [ 1179, 1223 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T19" } ] }, { "id": "8615697_E6", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to complex-type oligosaccharide units" ], "offsets": [ [ 1179, 1223 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T23" } ] }, { "id": "8615697_E7", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to complex-type oligosaccharide units" ], "offsets": [ [ 1179, 1223 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T22" } ] }, { "id": "8615697_E8", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to complex-type oligosaccharide units" ], "offsets": [ [ 1179, 1223 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T18" } ] }, { "id": "8615697_E9", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to complex-type oligosaccharide units" ], "offsets": [ [ 1179, 1223 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T21" } ] }, { "id": "8615697_E10", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "contain high mannose type units" ], "offsets": [ [ 1355, 1386 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T30" } ] }, { "id": "8615697_E11", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "contain high mannose type units" ], "offsets": [ [ 1355, 1386 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T31" } ] }, { "id": "8615697_E12", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "contain high mannose type units" ], "offsets": [ [ 1355, 1386 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T27" } ] }, { "id": "8615697_E13", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "contain high mannose type units" ], "offsets": [ [ 1355, 1386 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T29" } ] }, { "id": "8615697_E14", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "contain high mannose type units" ], "offsets": [ [ 1355, 1386 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T28" } ] }, { "id": "8615697_E15", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to oligosaccharide units" ], "offsets": [ [ 1433, 1464 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T34" } ] }, { "id": "8615697_E16", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "linked to oligosaccharide units" ], "offsets": [ [ 1433, 1464 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T33" } ] }, { "id": "8615697_E17", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 1857, 1869 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8615697_T7" }, { "role": "Site", "ref_id": "8615697_T37" } ] } ]

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[ { "id": "6587385__text", "type": "abstract", "text": [ "Amino acid sequence of porcine spleen cathepsin D. \nThe amino acid sequence of porcine spleen cathepsin D heavy chain has been determined and, hence, the complete structure of this enzyme is now known. The sequence of heavy chain was constructed by aligning the structures of peptides generated by cyanogen bromide, trypsin, and endo-proteinase Lys C cleavages. The structure of the light chain has been published previously. The cathepsin D molecule contains 339 amino acid residues in two polypeptide chains: a 97-residue light chain and a 242-residue heavy chain, with a combined Mr of 36,779 (without carbohydrate). There are two carbohydrate units linked to asparagine residues 70 and 192. The disulfide bond arrangement in cathepsin D is probably similar to that of pepsin, because the positions of six half-cystine residues are conserved. The active site aspartyl residues, corresponding to aspartic acid-32 and -215 of pepsin, are located at residues 33 and 224 in the cathepsin D molecule. The amino acid sequence around these aspartyl residues is strongly conserved. Cathepsin D shows a strong homology with other acid proteases. When the sequence of cathepsin D, renin, and pepsin are aligned, 32.7% of the residues are identical. The homology is observed throughout the length of the molecules, indicating that three-dimensional structures of all three molecules are similar. " ], "offsets": [ [ 0, 1388 ] ] } ]

[ { "id": "6587385_T1", "type": "Protein", "text": [ "cathepsin D" ], "offsets": [ [ 38, 49 ] ], "normalized": [] }, { "id": "6587385_T2", "type": "Protein", "text": [ "cathepsin D" ], "offsets": [ [ 94, 105 ] ], "normalized": [] }, { "id": "6587385_T3", "type": "Protein", "text": [ "cathepsin D" ], "offsets": [ [ 430, 441 ] ], "normalized": [] }, { "id": "6587385_T4", "type": "Protein", "text": [ "cathepsin D" ], "offsets": [ [ 729, 740 ] ], "normalized": [] }, { "id": "6587385_T5", "type": "Protein", "text": [ "cathepsin D" ], "offsets": [ [ 977, 988 ] ], "normalized": [] }, { "id": "6587385_T6", "type": "Protein", "text": [ "Cathepsin D" ], "offsets": [ [ 1077, 1088 ] ], "normalized": [] }, { "id": "6587385_T7", "type": "Protein", "text": [ "cathepsin D" ], "offsets": [ [ 1161, 1172 ] ], "normalized": [] }, { "id": "6587385_T9", "type": "Entity", "text": [ "asparagine residues 70" ], "offsets": [ [ 663, 685 ] ], "normalized": [] }, { "id": "6587385_T10", "type": "Entity", "text": [ "192" ], "offsets": [ [ 690, 693 ] ], "normalized": [] } ]

[ { "id": "6587385_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate units linked" ], "offsets": [ [ 634, 659 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6587385_T3" }, { "role": "Site", "ref_id": "6587385_T9" } ] }, { "id": "6587385_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate units linked" ], "offsets": [ [ 634, 659 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6587385_T3" }, { "role": "Site", "ref_id": "6587385_T10" } ] } ]

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[ { "id": "1451807__text", "type": "abstract", "text": [ "Natural human tumor necrosis factor beta (lymphotoxin). Variable O-glycosylation at Thr7, proteolytic processing, and allelic variation. \nNatural human tumor necrosis factor beta (TNF-beta) purified from supernatants of a human B-lymphoblastoid cell line was found to be heterogeneous in molecular mass, with seven components resolved by gel electrophoresis. All components are N-glycosylated at Asn62; N-glycosylation does not contribute to heterogeneity In addition, part of the molecules are O-glycosylated at Thr7; O-glycosylation is heterogeneous due to variable decoration with neuraminic acid. The four lower molecular mass forms are derived from the full-length protein by trypsin-like proteolytic cleavage in the N-proximal region; these clipped molecules lack O-linked carbohydrates. Two allelic variants differing in amino acid position 26 (threonine/asparagine) were identified. " ], "offsets": [ [ 0, 892 ] ] } ]

[ { "id": "1451807_T1", "type": "Protein", "text": [ "tumor necrosis factor beta" ], "offsets": [ [ 14, 40 ] ], "normalized": [] }, { "id": "1451807_T2", "type": "Protein", "text": [ "lymphotoxin" ], "offsets": [ [ 42, 53 ] ], "normalized": [] }, { "id": "1451807_T3", "type": "Protein", "text": [ "tumor necrosis factor beta" ], "offsets": [ [ 152, 178 ] ], "normalized": [] }, { "id": "1451807_T4", "type": "Protein", "text": [ "TNF-beta" ], "offsets": [ [ 180, 188 ] ], "normalized": [] }, { "id": "1451807_T6", "type": "Entity", "text": [ "Thr7" ], "offsets": [ [ 84, 88 ] ], "normalized": [] }, { "id": "1451807_T8", "type": "Entity", "text": [ "Thr7" ], "offsets": [ [ 514, 518 ] ], "normalized": [] } ]

[ { "id": "1451807_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "O-glycosylation" ], "offsets": [ [ 65, 80 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1451807_T1" }, { "role": "Site", "ref_id": "1451807_T6" } ] }, { "id": "1451807_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ " O-glycosylate" ], "offsets": [ [ 495, 509 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1451807_T3" }, { "role": "Site", "ref_id": "1451807_T8" } ] } ]

[ { "id": "1451807_1", "entity_ids": [ "1451807_T3", "1451807_T4" ] }, { "id": "1451807_2", "entity_ids": [ "1451807_T1", "1451807_T2" ] } ]

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[ { "id": "7240175__text", "type": "abstract", "text": [ "Complete amino acid sequence of a membrane receptor for glycoproteins. Sequence of the chicken hepatic lectin. \nThe chicken hepatic lectin is involved in the clearance of glycoproteins from circulation (Kawasaki, T., and Ashwell, G. (1977) J. Biol. Chem. 252, 6536-6543). The complete amino acid sequence of chicken hepatic lectin has been established by analysis of peptides generated by chemical cleavage at methionine or tryptophan residues. Larger BrCN fragments were further digested with trypsin, chymotrypsin, and clostripain. All sequences were determined by automated sequential Edman degradation. Extensive use was made of high performance liquid chromatography in the purification of peptides and identification of phenylthiohydantoin derivatives of amino acids. The complete sequence is: (formula: see text). The stretch of uncharged amino acids from residue 25 to 48 is a possible membrane-interaction region. Carbohydrate is attached to residue 67. " ], "offsets": [ [ 0, 963 ] ] } ]

[ { "id": "7240175_T1", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 103, 109 ] ], "normalized": [] }, { "id": "7240175_T2", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 132, 138 ] ], "normalized": [] }, { "id": "7240175_T3", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 324, 330 ] ], "normalized": [] }, { "id": "7240175_T4", "type": "Protein", "text": [ "trypsin" ], "offsets": [ [ 494, 501 ] ], "normalized": [] }, { "id": "7240175_T5", "type": "Protein", "text": [ "chymotrypsin" ], "offsets": [ [ 503, 515 ] ], "normalized": [] }, { "id": "7240175_T6", "type": "Protein", "text": [ "clostripain" ], "offsets": [ [ 521, 532 ] ], "normalized": [] }, { "id": "7240175_T8", "type": "Entity", "text": [ "residue 67" ], "offsets": [ [ 951, 961 ] ], "normalized": [] } ]

[ { "id": "7240175_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Carbohydrate is attached" ], "offsets": [ [ 923, 947 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7240175_T3" }, { "role": "Site", "ref_id": "7240175_T8" } ] } ]

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[ { "id": "6582489__text", "type": "abstract", "text": [ "Cloning of a cDNA encoding rat intestinal fatty acid binding protein. \nIntestinal fatty acid binding protein mRNA is one of the most abundant mRNA species in the rat small intestinal epithelium. RNA transfer blot analyses disclosed that the mRNA encoding intestinal fatty acid binding protein is approximately equal to 900 nucleotides long and not represented in liver RNA. We have identified 564 nucleotides of this mRNA, including 12 nucleotides of the 5' nontranslated region, the coding portion, and 155 nucleotides of the 3' nontranslated domain. The primary translation product encoded by this mRNA contains 132 amino acids and has a Mr of 15,062. The derived protein sequence was verified by automated sequential Edman degradation of the intact polypeptide isolated from a wheat germ cell-free system. The in vitro product is NH2-terminally acetylated, a finding that is consistent with its ultimate cytoplasmic destination. Comparison of the amino acid sequence of this protein with liver fatty acid binding protein, a polypeptide specified by the most abundant small intestinal epithelial mRNA, revealed significant homology and similarity in the predicted secondary structures of their NH2-terminal domains. " ], "offsets": [ [ 0, 1218 ] ] } ]

[ { "id": "6582489_T1", "type": "Protein", "text": [ "fatty acid binding protein" ], "offsets": [ [ 42, 68 ] ], "normalized": [] }, { "id": "6582489_T2", "type": "Protein", "text": [ "fatty acid binding protein" ], "offsets": [ [ 82, 108 ] ], "normalized": [] }, { "id": "6582489_T3", "type": "Protein", "text": [ "fatty acid binding protein" ], "offsets": [ [ 266, 292 ] ], "normalized": [] }, { "id": "6582489_T4", "type": "Protein", "text": [ "fatty acid binding protein" ], "offsets": [ [ 997, 1023 ] ], "normalized": [] }, { "id": "6582489_T5", "type": "Entity", "text": [ "NH2-terminally" ], "offsets": [ [ 833, 847 ] ], "normalized": [] } ]

[ { "id": "6582489_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 848, 858 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6582489_T3" }, { "role": "Site", "ref_id": "6582489_T5" } ] } ]

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[ { "id": "1388675__text", "type": "abstract", "text": [ "Rat liver low M(r) phosphotyrosine protein phosphatase isoenzymes: purification and amino acid sequences. \nTwo low M(r) phosphotyrosine protein phosphatases have been isolated from rat liver. The enzymes were previously known as low M(r) acid phosphatases, but several recent studies have demonstrated that this family of enzymes possesses specific phosphotyrosine protein phosphatase activity. We determined the complete amino acid sequences of the two isoenzymes and named them AcP1 and AcP2. Both consist of 157 amino acid residues, are acetylated at the NH2-terminus, and have His as the COOH-terminus. The molecular weights calculated from the sequences are 18,062 for AcP1 and 17,848 for AcP2. They are homologous except in the 40-73 zone, where about 50% of residues are different. This fact suggests that the two isoenzymes are produced by an alternative splicing mechanism. There is no homology between these two isoenzymes and the receptor-like phosphotyrosine protein phosphatases LAR, CD45, human placenta PTPase 1B, and rat brain PTPase-1. AcP1 and AcP2 are also distinct from rat liver PTPase-1 and PTPase-2, since these last enzymes have higher molecular weights. AcP1 differs from AcP2 with respect to (1) substrate affinity and (2) its sensitivity to activators and inhibitors, thus suggesting a their different physiological function. " ], "offsets": [ [ 0, 1354 ] ] } ]

[ { "id": "1388675_T1", "type": "Protein", "text": [ "AcP1" ], "offsets": [ [ 480, 484 ] ], "normalized": [] }, { "id": "1388675_T2", "type": "Protein", "text": [ "AcP2" ], "offsets": [ [ 489, 493 ] ], "normalized": [] }, { "id": "1388675_T3", "type": "Protein", "text": [ "AcP1" ], "offsets": [ [ 675, 679 ] ], "normalized": [] }, { "id": "1388675_T4", "type": "Protein", "text": [ "AcP2" ], "offsets": [ [ 695, 699 ] ], "normalized": [] }, { "id": "1388675_T5", "type": "Protein", "text": [ "LAR" ], "offsets": [ [ 993, 996 ] ], "normalized": [] }, { "id": "1388675_T6", "type": "Protein", "text": [ "CD45" ], "offsets": [ [ 998, 1002 ] ], "normalized": [] }, { "id": "1388675_T7", "type": "Protein", "text": [ "PTPase 1B" ], "offsets": [ [ 1019, 1028 ] ], "normalized": [] }, { "id": "1388675_T8", "type": "Protein", "text": [ "PTPase-1" ], "offsets": [ [ 1044, 1052 ] ], "normalized": [] }, { "id": "1388675_T9", "type": "Protein", "text": [ "AcP1" ], "offsets": [ [ 1054, 1058 ] ], "normalized": [] }, { "id": "1388675_T10", "type": "Protein", "text": [ "AcP2" ], "offsets": [ [ 1063, 1067 ] ], "normalized": [] }, { "id": "1388675_T11", "type": "Protein", "text": [ "PTPase-1" ], "offsets": [ [ 1101, 1109 ] ], "normalized": [] }, { "id": "1388675_T12", "type": "Protein", "text": [ "PTPase-2" ], "offsets": [ [ 1114, 1122 ] ], "normalized": [] }, { "id": "1388675_T13", "type": "Protein", "text": [ "AcP1" ], "offsets": [ [ 1180, 1184 ] ], "normalized": [] }, { "id": "1388675_T14", "type": "Protein", "text": [ "AcP2" ], "offsets": [ [ 1198, 1202 ] ], "normalized": [] }, { "id": "1388675_T16", "type": "Entity", "text": [ "His" ], "offsets": [ [ 581, 584 ] ], "normalized": [] } ]

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[ { "id": "2964863__text", "type": "abstract", "text": [ "Primary structure of human placental anticoagulant protein. \nThe primary structure of human placental anticoagulant protein was determined by a combination of amino acid and nucleotide sequencing techniques. The carboxymethylated protein was digested with cyanogen bromide, and the resulting peptides were separated by gel filtration and high-performance liquid chromatography. A total of 239 out of 319 amino acid residues were identified from 7 cyanogen bromide fragments. A full-length cDNA clone encoding placental anticoagulant protein was isolated from a human placenta cDNA library. This clone was 1.6 kilobases long and contained a translation initiation site coding for methionine, 957 nucleotides encoding for the mature protein, a stop codon, a poly(A) recognition site, and a poly(A) tail. Analysis of the tryptic-blocked peptide that originated from the NH2-terminus of the protein showed that the terminal methionine was removed and the adjacent alanine residue was acetylated by posttranslational events. Placental anticoagulant protein is composed of 319 amino acids with acetylalanine as the NH2-terminus and has a high degree of sequence identity with lipocortins I and II. It contains four internal repeats, each including a sequence corresponding to a putative Ca2+-dependent phospholipid binding site. Placental anticoagulant protein is a member of the lipocortin/calpactin family. " ], "offsets": [ [ 0, 1403 ] ] } ]

[ { "id": "2964863_T1", "type": "Protein", "text": [ "placental anticoagulant protein" ], "offsets": [ [ 27, 58 ] ], "normalized": [] }, { "id": "2964863_T2", "type": "Protein", "text": [ "placental anticoagulant protein" ], "offsets": [ [ 92, 123 ] ], "normalized": [] }, { "id": "2964863_T3", "type": "Protein", "text": [ "placental anticoagulant protein" ], "offsets": [ [ 509, 540 ] ], "normalized": [] }, { "id": "2964863_T4", "type": "Protein", "text": [ "Placental anticoagulant protein" ], "offsets": [ [ 1020, 1051 ] ], "normalized": [] }, { "id": "2964863_T5", "type": "Protein", "text": [ "Placental anticoagulant protei" ], "offsets": [ [ 1323, 1353 ] ], "normalized": [] }, { "id": "2964863_T6", "type": "Entity", "text": [ "terminal methionine" ], "offsets": [ [ 911, 930 ] ], "normalized": [] } ]

[ { "id": "2964863_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 980, 990 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2964863_T3" }, { "role": "Site", "ref_id": "2964863_T6" } ] } ]

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[ { "id": "6723659__text", "type": "abstract", "text": [ "Aldehyde dehydrogenase from human liver. Primary structure of the cytoplasmic isoenzyme. \nAnalysis of CNBr fragments and other peptides from human liver cytoplasmic aldehyde dehydrogenase enabled determination of the complete primary structure of this protein. The monomer has an acylated amino terminus and is composed of 500 amino acid residues, including 11 cysteine residues. No evidence of any microheterogeneity was obtained, supporting the concept that the enzyme is a homotetramer . The disulfiram-sensitive thiol in the protein, earlier identified through its reaction with iodoacetamide, is contributed by a cysteine residue at position 302, while the cysteine which in horse liver mitochondrial aldehyde dehydrogenase is reactive with coenzyme analogs appears to correspond to either Cys-455 or Cys-463. Analysis of glycine distribution and prediction of secondary structures to localize beta alpha beta regions typical for coenzyme-binding are not fully unambiguous, but suggest a short region around position 245 as a likely segment for this function. In this region, sequence similarities to parts of a bacterial aspartate-beta-semialdehyde dehydrogenase and a mammalian alcohol dehydrogenase were noted. Otherwise, no extensive similarities were detected in comparisons with characterized mammalian enzymes of similar activity or subunit size as aldehyde dehydrogenase (glyceraldehyde-3-phosphate dehydrogenase and glutamate dehydrogenase, respectively). " ], "offsets": [ [ 0, 1470 ] ] } ]

[ { "id": "6723659_T1", "type": "Protein", "text": [ "Aldehyde dehydrogenase" ], "offsets": [ [ 0, 22 ] ], "normalized": [] }, { "id": "6723659_T2", "type": "Protein", "text": [ "aldehyde dehydrogenase" ], "offsets": [ [ 165, 187 ] ], "normalized": [] }, { "id": "6723659_T3", "type": "Protein", "text": [ "aldehyde dehydrogenase" ], "offsets": [ [ 706, 728 ] ], "normalized": [] }, { "id": "6723659_T4", "type": "Protein", "text": [ "aspartate-beta-semialdehyde dehydrogenase" ], "offsets": [ [ 1127, 1168 ] ], "normalized": [] }, { "id": "6723659_T5", "type": "Protein", "text": [ "aldehyde dehydrogenase" ], "offsets": [ [ 1361, 1383 ] ], "normalized": [] }, { "id": "6723659_T6", "type": "Protein", "text": [ "glyceraldehyde-3-phosphate dehydrogenase" ], "offsets": [ [ 1385, 1425 ] ], "normalized": [] }, { "id": "6723659_T7", "type": "Protein", "text": [ "glutamate dehydrogenase" ], "offsets": [ [ 1430, 1453 ] ], "normalized": [] }, { "id": "6723659_T9", "type": "Entity", "text": [ "amino terminus" ], "offsets": [ [ 289, 303 ] ], "normalized": [] } ]

[ { "id": "6723659_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "has an acylated amino terminus" ], "offsets": [ [ 273, 303 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6723659_T2" }, { "role": "Site", "ref_id": "6723659_T9" } ] } ]

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[ { "id": "6820420__text", "type": "abstract", "text": [ "Normal hydroxylation of proline in collagen synthesized by skin fibroblasts from a patient with prolidase deficiency. \nThe extent of hydroxylation of proline in collagen synthesized and secreted into the culture medium by skin fibroblasts derived from a patient with prolidase deficiency has been examined and found to be normal. It would seem likely that to a considerable extent the urinary proline-containing dipeptides apparent in this condition are derived from sources other than collagen. " ], "offsets": [ [ 0, 496 ] ] } ]

[ { "id": "6820420_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 35, 43 ] ], "normalized": [] }, { "id": "6820420_T2", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 161, 169 ] ], "normalized": [] }, { "id": "6820420_T3", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 486, 494 ] ], "normalized": [] }, { "id": "6820420_T5", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 24, 31 ] ], "normalized": [] }, { "id": "6820420_T7", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 150, 157 ] ], "normalized": [] } ]

[ { "id": "6820420_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 7, 20 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6820420_T1" }, { "role": "Site", "ref_id": "6820420_T5" } ] }, { "id": "6820420_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 133, 146 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6820420_T2" }, { "role": "Site", "ref_id": "6820420_T7" } ] } ]

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[ { "id": "4141893__text", "type": "abstract", "text": [ "Amino acid sequence of the smaller basic protein from rat brain myelin. \n3. An arginine residue in the rat protein was found to be partially methylated. " ], "offsets": [ [ 0, 153 ] ] } ]

[ { "id": "4141893_T1", "type": "Protein", "text": [ "myelin" ], "offsets": [ [ 64, 70 ] ], "normalized": [] }, { "id": "4141893_T2", "type": "Entity", "text": [ "arginine" ], "offsets": [ [ 79, 87 ] ], "normalized": [] } ]

[ { "id": "4141893_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "y methylat" ], "offsets": [ [ 139, 149 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4141893_T1" }, { "role": "Site", "ref_id": "4141893_T2" } ] } ]

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[ { "id": "3782055__text", "type": "abstract", "text": [ "Human spleen histone H1. Isolation and amino acid sequence of a main variant, H1b. \nThe complete amino acid sequence of a main variant, H1b, of human spleen histone H1 was determined, following previous determinations of human spleen histones H2B, H2A, H3, and H4. High-performance liquid chromatography on C8 silica of the H1 fraction yielded the homogeneous H1b subfraction; this variant was estimated to account for 60% of the total of the four H1 variants. The sequence determination was performed with four main fragments, I to IV, obtained by limited chymotryptic digestion of H1b. Together with direct sequencing by automated Edman degradation of fragments II, III, and IV, fragment I, blocked at the N-terminal, and fragment IV, the C-terminal half the H1b molecule, were sequenced after further digestion with staphylococcal protease and others. The four fragments were aligned with three overlapping peptides each derived from chymotryptic partial fragments, I-II and I-II-III, and intact H1b. Carboxypeptidase digestion of intact H1b confirmed the C-terminal sequence of the molecule. Thus, the total sequence of H1b was completely determined; it consists of a total of 218 amino acid residues, has a molecular weight of 21,734 in the unmodified form, and is completely acetylated at the N-terminal serine residue and partially methylated at the lysine residue 25. This sequence is compared with two mammalian somatic H1 sequences. " ], "offsets": [ [ 0, 1450 ] ] } ]

[ { "id": "3782055_T1", "type": "Protein", "text": [ "histone H1" ], "offsets": [ [ 13, 23 ] ], "normalized": [] }, { "id": "3782055_T2", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 78, 81 ] ], "normalized": [] }, { "id": "3782055_T3", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 136, 139 ] ], "normalized": [] }, { "id": "3782055_T4", "type": "Protein", "text": [ "histone H1" ], "offsets": [ [ 157, 167 ] ], "normalized": [] }, { "id": "3782055_T5", "type": "Protein", "text": [ " histones H2B" ], "offsets": [ [ 233, 246 ] ], "normalized": [] }, { "id": "3782055_T6", "type": "Protein", "text": [ "H2A" ], "offsets": [ [ 248, 251 ] ], "normalized": [] }, { "id": "3782055_T7", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 253, 255 ] ], "normalized": [] }, { "id": "3782055_T8", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 261, 263 ] ], "normalized": [] }, { "id": "3782055_T9", "type": "Protein", "text": [ "H1" ], "offsets": [ [ 325, 327 ] ], "normalized": [] }, { "id": "3782055_T10", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 361, 364 ] ], "normalized": [] }, { "id": "3782055_T11", "type": "Protein", "text": [ "H1" ], "offsets": [ [ 449, 451 ] ], "normalized": [] }, { "id": "3782055_T12", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 585, 588 ] ], "normalized": [] }, { "id": "3782055_T13", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 764, 767 ] ], "normalized": [] }, { "id": "3782055_T14", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 1003, 1006 ] ], "normalized": [] }, { "id": "3782055_T15", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 1046, 1049 ] ], "normalized": [] }, { "id": "3782055_T16", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 1130, 1133 ] ], "normalized": [] }, { "id": "3782055_T17", "type": "Protein", "text": [ "H1" ], "offsets": [ [ 1436, 1438 ] ], "normalized": [] }, { "id": "3782055_T19", "type": "Entity", "text": [ "N-terminal serine residue" ], "offsets": [ [ 1305, 1330 ] ], "normalized": [] }, { "id": "3782055_T20", "type": "Entity", "text": [ "serine" ], "offsets": [ [ 1316, 1322 ] ], "normalized": [] }, { "id": "3782055_T22", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 1363, 1369 ] ], "normalized": [] }, { "id": "3782055_T23", "type": "Entity", "text": [ "lysine residue 25" ], "offsets": [ [ 1363, 1380 ] ], "normalized": [] } ]

[ { "id": "3782055_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 1287, 1297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3782055_T16" }, { "role": "Site", "ref_id": "3782055_T20" } ] }, { "id": "3782055_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 1345, 1355 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3782055_T16" }, { "role": "Site", "ref_id": "3782055_T22" } ] } ]

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[ { "id": "7798168__text", "type": "abstract", "text": [ "Purification and amino- and carboxyl-terminal amino acid sequences of alanine-glyoxylate transaminase 1 from human liver. \nIn order to confirm the amino acid sequence predicted from the nucleotide sequence of cDNA and also to elucidate the intracellular localization and molecular evolution, human liver alanine-glyoxylate transaminase 1 (AGT1) was purified and subjected to partial amino acid sequence determination, with special attention to posttranslational modification. The enzyme was purified to homogeneity from the 10,000 x g supernatant of human liver homogenate. The purified enzyme showed only a single protein band at about 43 kDa on SDS-PAGE, indicating that it is a homodimer of two identical subunits, because the native enzyme has a molecular mass of about 80 kDa. Both the amino- and carboxyl-terminal peptides of the enzyme were isolated from a cyanogen bromide digest of the S-carboxyl-methylated protein and subjected to amino acid sequence determination. The alpha-amino group of the amino-terminal peptide was shown to be blocked by an acetyl group. The carboxyl-terminal sequence contained a putative N-glycosylation sequence (-Asn-Ala-Thr-), the only one present in the whole molecule, but this sequence was normally determined, indicating that the enzyme is not N-glycosylated. Purdue et al. [J. Cell Biol. 111, 2341-2351 (1990)] have reported that Pro-11, Gly-170, and Ile-340 in normal human AGT1 were replaced by Leu, Arg, and Met, respectively, in a patient with primary hyperoxaluria type 1. We confirmed that residue-11 was Pro. Both the amino- and carboxyl-terminal sequences of the enzyme showed extensive similarity with those of rat liver mitochondrial serine-pyruvate aminotransferase and the small chain of hydrogenase from a thermophilic unicellular cyanobacterium, Synechococcus PCC 6716. (ABSTRACT TRUNCATED AT 250 WORDS) " ], "offsets": [ [ 0, 1863 ] ] } ]

[ { "id": "7798168_T1", "type": "Protein", "text": [ "alanine-glyoxylate transaminase 1" ], "offsets": [ [ 70, 103 ] ], "normalized": [] }, { "id": "7798168_T2", "type": "Protein", "text": [ "alanine-glyoxylate transaminase 1" ], "offsets": [ [ 304, 337 ] ], "normalized": [] }, { "id": "7798168_T3", "type": "Protein", "text": [ "AGT1" ], "offsets": [ [ 339, 343 ] ], "normalized": [] }, { "id": "7798168_T4", "type": "Entity", "text": [ "amino-terminal peptide" ], "offsets": [ [ 1006, 1028 ] ], "normalized": [] } ]

[ { "id": "7798168_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked by an acetyl group" ], "offsets": [ [ 1045, 1071 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7798168_T3" }, { "role": "Site", "ref_id": "7798168_T4" } ] } ]

[ { "id": "7798168_1", "entity_ids": [ "7798168_T3", "7798168_T2" ] } ]

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[ { "id": "6296823__text", "type": "abstract", "text": [ "Conformational implications of enzymatic proline hydroxylation in collagen. \nIn 1979 it was proposed that prolyl hydroxylase (prolyl-glycyl-peptide,2-oxoglutarate:oxygen oxidoreductase, EC 1.14.11.2) recognizes the beta-turn conformation in nascent procollagen chains and that the hydroxylation process involves a conformational change resulting in \"straightening\" of the beta-turn segments into the linear triple-helical conformation of native collagen. We present experimental data that verify both these postulates. The following peptides were synthesized and studied for their conformation and interaction with prolyl hydroxylase: tBoc-Pro-Gly-Ala-OH, tBoc-Pro-Gly-Val-OH, tBoc-Gly-Val-Pro-Gly-Val-OH, and tBoc-Pro-DAla-Ala-OH. Spectral data showed that these peptides preferred a beta-turn conformation. All of them acted as inhibitors of the enzyme; the pentapeptide also acted as a substrate. To mimic the biosynthetic event, a collagen model polypeptide, (Pro-Pro-Gly)10, was incubated at 37 degrees C with purified prolyl hydroxylase and the necessary cosubstrates and cofactors at pH 7.8. A progressive change from the initially nonhelical to the triple-helical conformation, as monitored by CD spectra and gel filtration, occurred during the course of proline hydroxylation. In addition to leading to increased thermal stability of the triple-helical conformation in (Pro-Pro-Gly)10 and (Pro-Pro-Gly)5, the enzymatic incorporation of the hydroxyproline residues was found to enable these polypeptides to fold into this conformation faster than the unhydroxylated counterparts. These conformational implications of proline hydroxylation in collagen may also be of use in the study of the complement subcomponent Clq and of acetylcholine esterase which contain collagen-like regions in them. " ], "offsets": [ [ 0, 1801 ] ] } ]

[ { "id": "6296823_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 66, 74 ] ], "normalized": [] }, { "id": "6296823_T2", "type": "Protein", "text": [ "procollagen" ], "offsets": [ [ 249, 260 ] ], "normalized": [] }, { "id": "6296823_T3", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 445, 453 ] ], "normalized": [] }, { "id": "6296823_T4", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 935, 943 ] ], "normalized": [] }, { "id": "6296823_T5", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 1650, 1658 ] ], "normalized": [] }, { "id": "6296823_T6", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 41, 48 ] ], "normalized": [] }, { "id": "6296823_T8", "type": "Entity", "text": [ "prolyl" ], "offsets": [ [ 106, 112 ] ], "normalized": [] }, { "id": "6296823_T10", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 1263, 1270 ] ], "normalized": [] }, { "id": "6296823_T12", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 1625, 1632 ] ], "normalized": [] } ]

[ { "id": "6296823_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 49, 62 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6296823_T1" }, { "role": "Site", "ref_id": "6296823_T6" } ] }, { "id": "6296823_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 281, 294 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6296823_T3" }, { "role": "Site", "ref_id": "6296823_T8" } ] }, { "id": "6296823_E3", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1271, 1284 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6296823_T4" }, { "role": "Site", "ref_id": "6296823_T10" } ] }, { "id": "6296823_E4", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1633, 1646 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6296823_T5" }, { "role": "Site", "ref_id": "6296823_T12" } ] } ]

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[ { "id": "3421901__text", "type": "abstract", "text": [ "Characterization and amino acid sequence of a fatty acid-binding protein from human heart. \nThe complete amino acid sequence of a fatty acid-binding protein from human heart was determined by automated Edman degradation of CNBr, BNPS-skatole [3'-bromo-3-methyl-2-(2-nitrobenzenesulphenyl)indolenine], hydroxylamine, Staphylococcus aureus V8 proteinase, tryptic and chymotryptic peptides, and by digestion of the protein with carboxypeptidase A. The sequence of the blocked N-terminal tryptic peptide from citraconylated protein was determined by collisionally induced decomposition mass spectrometry. The protein contains 132 amino acid residues, is enriched with respect to threonine and lysine, lacks cysteine, has an acetylated valine residue at the N-terminus, and has an Mr of 14768 and an isoelectric point of 5.25. This protein contains two short internal repeated sequences from residues 48-54 and from residues 114-119 located within regions of predicted beta-structure and decreasing hydrophobicity. These short repeats are contained within two longer repeated regions from residues 48-60 and residues 114-125, which display 62% sequence similarity. These regions could accommodate the charged and uncharged moieties of long-chain fatty acids and may represent fatty acid-binding domains consistent with the finding that human heart fatty acid-binding protein binds 2 mol of oleate or palmitate/mol of protein. Detailed evidence for the amino acid sequences of the peptides has been deposited as Supplementary Publication SUP 50143 (23 pages) at the British Library Lending Division, Boston Spa, Yorkshire LS23 7BQ, U.K., from whom copies may be obtained as indicated in Biochem. J. (1988) 249, 5. " ], "offsets": [ [ 0, 1708 ] ] } ]

[ { "id": "3421901_T1", "type": "Protein", "text": [ "fatty acid-binding protein" ], "offsets": [ [ 46, 72 ] ], "normalized": [] }, { "id": "3421901_T2", "type": "Protein", "text": [ "fatty acid-binding protein" ], "offsets": [ [ 130, 156 ] ], "normalized": [] }, { "id": "3421901_T3", "type": "Protein", "text": [ "V8 proteinase" ], "offsets": [ [ 338, 351 ] ], "normalized": [] }, { "id": "3421901_T4", "type": "Protein", "text": [ "carboxypeptidase A" ], "offsets": [ [ 425, 443 ] ], "normalized": [] }, { "id": "3421901_T6", "type": "Entity", "text": [ "valine" ], "offsets": [ [ 731, 737 ] ], "normalized": [] } ]

[ { "id": "3421901_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 720, 730 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3421901_T2" }, { "role": "Site", "ref_id": "3421901_T6" } ] } ]

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[ { "id": "8506377__text", "type": "abstract", "text": [ "Isolation and the complete amino acid sequence of lumenal endoplasmic reticulum glucose-6-phosphate dehydrogenase. \nI have isolated glucose-6-phosphate dehydrogenase from rabbit liver microsomes and determined its complete amino acid sequence. Sequence determination was achieved by automated Edman degradation of peptides generated by chemical and enzymatic cleavages. The microsomal enzyme consists of 763 residues and is quite dissimilar from the previously characterized cytosolic enzymes. The N terminus of the microsomal enzyme is blocked by a pyroglutamyl residue. Carbohydrate is attached at Asn-138 and Asn-263, implying that the bulk of the protein is oriented on the lumenal side of the endoplasmic membrane. The amino acid sequence of the microsomal protein shows limited homology to the extensively sequenced cytosolic glucose-6-phosphate dehydrogenases. Clusters of up to six identical residues can be identified in four regions: peptide segments at residues 10-21, 154-163, and 173-261. In addition, another array of identical residues, requiring a 100-residue deletion in the sequence of the microsomal enzyme, spans residues 436-462 and corresponds to residues 348-373 of the cytosolic protein. Two segments with a Gly-Xaa-Gly-Xaa-Xaa-Gly motif, related to a coenzyme binding fold, were identified at Gly-399 and Gly-491. In the cytosolic enzymes, a variation of this sequence motif occurs at Gly-37 and Gly-241. The 300-residue C-terminal segment of the microsomal enzyme is unique and has no counterpart in the cytosolic or the bacterial enzymes. An unexpected finding with regard to the microsomal enzyme is that it lacks an identifiable membrane-spanning region or the lumenal-protein C-terminal consensus sequences Lys-Asp-Glu or His-Ile/Thr-Glu-Leu. Thus, the mode of transport and retention of this protein in the lumen of endoplasmic reticulum remains to be determined. " ], "offsets": [ [ 0, 1895 ] ] } ]

[ { "id": "8506377_T1", "type": "Protein", "text": [ "glucose-6-phosphate dehydrogenase" ], "offsets": [ [ 80, 113 ] ], "normalized": [] }, { "id": "8506377_T2", "type": "Protein", "text": [ "glucose-6-phosphate dehydrogenase" ], "offsets": [ [ 132, 165 ] ], "normalized": [] }, { "id": "8506377_T3", "type": "Protein", "text": [ "glucose-6-phosphate dehydrogenases" ], "offsets": [ [ 832, 866 ] ], "normalized": [] }, { "id": "8506377_T5", "type": "Entity", "text": [ "Asn-138" ], "offsets": [ [ 600, 607 ] ], "normalized": [] }, { "id": "8506377_T6", "type": "Entity", "text": [ "Asn-263" ], "offsets": [ [ 612, 619 ] ], "normalized": [] } ]

[ { "id": "8506377_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Carbohydrate is attached" ], "offsets": [ [ 572, 596 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8506377_T2" }, { "role": "Site", "ref_id": "8506377_T5" } ] }, { "id": "8506377_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Carbohydrate is attached" ], "offsets": [ [ 572, 596 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8506377_T2" }, { "role": "Site", "ref_id": "8506377_T6" } ] } ]

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[ { "id": "3606579__text", "type": "abstract", "text": [ "The primary structure of histone H2A from the nematode Caenorhabditis elegans. \nThe complete primary structure of histone H2A from the nematode Caenorhabditis elegans was determined. The amino acid chain consists of 126 amino acid residues and has a blocked N-terminus. By comparison with calf thymus histone H2A, the nematode protein shows five deletions, two insertions and 16 substitutions. Most of the changes occur in the N- and C-terminal regions of the molecule, whereas the central part covering the residues 21-120 is quite well conserved. The lysine residues 5, 8 and 10 were found to be partially acetylated. " ], "offsets": [ [ 0, 620 ] ] } ]

[ { "id": "3606579_T1", "type": "Protein", "text": [ "histone H2A" ], "offsets": [ [ 25, 36 ] ], "normalized": [] }, { "id": "3606579_T2", "type": "Protein", "text": [ "histone H2A" ], "offsets": [ [ 114, 125 ] ], "normalized": [] }, { "id": "3606579_T3", "type": "Protein", "text": [ "histone H2A" ], "offsets": [ [ 301, 312 ] ], "normalized": [] }, { "id": "3606579_T4", "type": "Entity", "text": [ "126 amino acid residues" ], "offsets": [ [ 216, 239 ] ], "normalized": [] }, { "id": "3606579_T6", "type": "Entity", "text": [ "lysine residues 5" ], "offsets": [ [ 553, 570 ] ], "normalized": [] }, { "id": "3606579_T7", "type": "Entity", "text": [ "8" ], "offsets": [ [ 572, 573 ] ], "normalized": [] }, { "id": "3606579_T8", "type": "Entity", "text": [ "10" ], "offsets": [ [ 578, 580 ] ], "normalized": [] } ]

[ { "id": "3606579_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "has a blocked N-terminus" ], "offsets": [ [ 244, 268 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3606579_T2" }, { "role": "Site", "ref_id": "3606579_T4" } ] }, { "id": "3606579_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "partially acetylated" ], "offsets": [ [ 598, 618 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3606579_T2" }, { "role": "Site", "ref_id": "3606579_T6" } ] }, { "id": "3606579_E3", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "partially acetylated" ], "offsets": [ [ 598, 618 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3606579_T2" }, { "role": "Site", "ref_id": "3606579_T8" } ] }, { "id": "3606579_E4", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "partially acetylated" ], "offsets": [ [ 598, 618 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3606579_T2" }, { "role": "Site", "ref_id": "3606579_T7" } ] } ]

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[ { "id": "173531__text", "type": "abstract", "text": [ "The covalent structure of collagen. The amino-acid sequence of alpha2-CB4 from calf-skin collagen. \nSequencing of chymotrypsin, trypsin, collagenase- and hydroxylamine-derived peptides, using the automated Edman degradation procedure, yielded the complete amino acid sequence of alpha2-CB4 from calf skin collagen (321 residues). Together with the data from earlier work, an uninterrupted sequence in the helical region of the alpha2-chain from residues 1-393 is now known. Glycine is found in every third position of the peptide. Hydroxylation of proline and lysine occurs only in the Y-position of the triplet Gly-X-Y and is not complete in every position. Some residues, such as glutamic acid, leucine, phenylalanine and arginine, are distributed non-randomly between the X and Y-positions and this non-random distribution is different in the alpha1 and alpha2-chains. Comparison of the N-terminal 393 residues from the helical region of the alpha1 and alpha2-chains revealed a nearly identical distribution of charged polar residues arginine, lysine, glutamic and aspartic acids. The distribution of the triplet Gly-Pro-Hyp is simialr in both chains. The remaining residues in the alpha2-chain exhibit a high degree of substitutions when compared with those in the alpha1-chain. Approximately one in every two residues in both the X and Y-positions are substituted. " ], "offsets": [ [ 0, 1378 ] ] } ]

[ { "id": "173531_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 26, 34 ] ], "normalized": [] }, { "id": "173531_T2", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 90, 98 ] ], "normalized": [] }, { "id": "173531_T3", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 306, 314 ] ], "normalized": [] }, { "id": "173531_T4", "type": "Entity", "text": [ "calf skin collagen" ], "offsets": [ [ 296, 314 ] ], "normalized": [] }, { "id": "173531_T6", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 551, 558 ] ], "normalized": [] }, { "id": "173531_T7", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 563, 569 ] ], "normalized": [] } ]

[ { "id": "173531_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ " Hydroxylatio" ], "offsets": [ [ 533, 546 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "173531_T3" }, { "role": "Site", "ref_id": "173531_T6" } ] }, { "id": "173531_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ " Hydroxylatio" ], "offsets": [ [ 533, 546 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "173531_T3" }, { "role": "Site", "ref_id": "173531_T7" } ] } ]

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[ { "id": "8323299__text", "type": "abstract", "text": [ "Assignment of O-glycan attachment sites to the hinge-like regions of human lysosomal membrane glycoproteins lamp-1 and lamp-2. \nThe lysosomal membrane glycoproteins lamp-1 and lamp-2 are extensively glycosylated with a variety of different carbohydrate structures of both N-linked and O-linked type. In the present paper, we report the localization of O-linked oligosaccharides exclusively to the hinge-like regions of lamp-1 and lamp-2 isolated from human chronic myelogenous leukemia cells. In both glycoproteins, the O-glycans appear in clusters. In lamp-1, Thr-171, Thr-172, Ser-179, Ser-181, and Ser-183 were fully glycosylated, whereas Ser-169 was partially glycosylated. In lamp-2, complete glycosylation was found at Ser-167, Thr-168, Thr-172, Thr-175, Thr-176, Thr-182, and Thr-183, and partial glycosylation at Ser-179 and Thr-181, and possibly also at Thr-185. The amino acid sequences of these O-glycosylation sites are consistent with the previous reports that residues at positions -1 and +3 may influence the glycosylation reaction. Circular dichroism and nuclear magnetic resonance spectroscopy was used for the structural characterization of a synthetic peptide corresponding to residues 167 to 190 of lamp-1. The results indicated that the proline-rich O-glycan acceptor region does not adopt any typical periodic structure but differs from random-coil structure. The circular dichroism spectrum of the peptide is, however, similar to that of porcine submaxillary apomucin. A significant conformational variability was observed in this region, presumably due to a slow (on the nuclear magnetic resonance time scale) cis-trans isomerization of several proline residues. These results, taken together, strongly suggest that a hinge region does not display any typical ordered structure. The presence of O-glycans thus likely protects this region from intralumenal lysosomal proteases. " ], "offsets": [ [ 0, 1901 ] ] } ]

[ { "id": "8323299_T1", "type": "Protein", "text": [ "lamp-1" ], "offsets": [ [ 108, 114 ] ], "normalized": [] }, { "id": "8323299_T2", "type": "Protein", "text": [ "lamp-2" ], "offsets": [ [ 119, 125 ] ], "normalized": [] }, { "id": "8323299_T3", "type": "Protein", "text": [ "lamp-1" ], "offsets": [ [ 165, 171 ] ], "normalized": [] }, { "id": "8323299_T4", "type": "Protein", "text": [ "lamp-2" ], "offsets": [ [ 176, 182 ] ], "normalized": [] }, { "id": "8323299_T5", "type": "Protein", "text": [ "lamp-1" ], "offsets": [ [ 419, 425 ] ], "normalized": [] }, { "id": "8323299_T6", "type": "Protein", "text": [ "lamp-2" ], "offsets": [ [ 430, 436 ] ], "normalized": [] }, { "id": "8323299_T7", "type": "Protein", "text": [ "lamp-1" ], "offsets": [ [ 553, 559 ] ], "normalized": [] }, { "id": "8323299_T8", "type": "Protein", "text": [ "lamp-2" ], "offsets": [ [ 681, 687 ] ], "normalized": [] }, { "id": "8323299_T9", "type": "Protein", "text": [ "lamp-1" ], "offsets": [ [ 1219, 1225 ] ], "normalized": [] }, { "id": "8323299_T10", "type": "Entity", "text": [ "Thr-171" ], "offsets": [ [ 561, 568 ] ], "normalized": [] }, { "id": "8323299_T11", "type": "Entity", "text": [ "Thr-172" ], "offsets": [ [ 570, 577 ] ], "normalized": [] }, { "id": "8323299_T12", "type": "Entity", "text": [ "Ser-179" ], "offsets": [ [ 579, 586 ] ], "normalized": [] }, { "id": "8323299_T13", "type": "Entity", "text": [ "Ser-181" ], "offsets": [ [ 588, 595 ] ], "normalized": [] }, { "id": "8323299_T14", "type": "Entity", "text": [ "Ser-183" ], "offsets": [ [ 601, 608 ] ], "normalized": [] }, { "id": "8323299_T16", "type": "Entity", "text": [ "Ser-169" ], "offsets": [ [ 642, 649 ] ], "normalized": [] }, { "id": "8323299_T19", "type": "Entity", "text": [ "Ser-167" ], "offsets": [ [ 725, 732 ] ], "normalized": [] }, { "id": "8323299_T20", "type": "Entity", "text": [ "Thr-168" ], "offsets": [ [ 734, 741 ] ], "normalized": [] }, { "id": "8323299_T21", "type": "Entity", "text": [ "Thr-172" ], "offsets": [ [ 743, 750 ] ], "normalized": [] }, { "id": "8323299_T22", "type": "Entity", "text": [ "Thr-175" ], "offsets": [ [ 752, 759 ] ], "normalized": [] }, { "id": "8323299_T23", "type": "Entity", "text": [ "Thr-176" ], "offsets": [ [ 761, 768 ] ], "normalized": [] }, { "id": "8323299_T24", "type": "Entity", "text": [ "Thr-182" ], "offsets": [ [ 770, 777 ] ], "normalized": [] }, { "id": "8323299_T25", "type": "Entity", "text": [ "Thr-183" ], "offsets": [ [ 783, 790 ] ], "normalized": [] }, { "id": "8323299_T27", "type": "Entity", "text": [ "Ser-179" ], "offsets": [ [ 821, 828 ] ], "normalized": [] }, { "id": "8323299_T28", "type": "Entity", "text": [ "Thr-181" ], "offsets": [ [ 833, 840 ] ], "normalized": [] }, { "id": "8323299_T29", "type": "Entity", "text": [ "Thr-185" ], "offsets": [ [ 863, 870 ] ], "normalized": [] } ]

[ { "id": "8323299_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "fully glycosylated" ], "offsets": [ [ 614, 632 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T7" }, { "role": "Site", "ref_id": "8323299_T10" } ] }, { "id": "8323299_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "fully glycosylated" ], "offsets": [ [ 614, 632 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T7" }, { "role": "Site", "ref_id": "8323299_T13" } ] }, { "id": "8323299_E3", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "fully glycosylated" ], "offsets": [ [ 614, 632 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T7" }, { "role": "Site", "ref_id": "8323299_T12" } ] }, { "id": "8323299_E4", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "fully glycosylated" ], "offsets": [ [ 614, 632 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T7" }, { "role": "Site", "ref_id": "8323299_T11" } ] }, { "id": "8323299_E5", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "fully glycosylated" ], "offsets": [ [ 614, 632 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T7" }, { "role": "Site", "ref_id": "8323299_T14" } ] }, { "id": "8323299_E6", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "partially glycosylated" ], "offsets": [ [ 654, 676 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T7" }, { "role": "Site", "ref_id": "8323299_T16" } ] }, { "id": "8323299_E7", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "complete glycosylation" ], "offsets": [ [ 689, 711 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T24" } ] }, { "id": "8323299_E8", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "complete glycosylation" ], "offsets": [ [ 689, 711 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T25" } ] }, { "id": "8323299_E9", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "complete glycosylation" ], "offsets": [ [ 689, 711 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T20" } ] }, { "id": "8323299_E10", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "complete glycosylation" ], "offsets": [ [ 689, 711 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T21" } ] }, { "id": "8323299_E11", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "complete glycosylation" ], "offsets": [ [ 689, 711 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T23" } ] }, { "id": "8323299_E12", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "complete glycosylation" ], "offsets": [ [ 689, 711 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T19" } ] }, { "id": "8323299_E13", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "complete glycosylation" ], "offsets": [ [ 689, 711 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T22" } ] }, { "id": "8323299_E14", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "partial glycosylation" ], "offsets": [ [ 796, 817 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T28" } ] }, { "id": "8323299_E15", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "partial glycosylation" ], "offsets": [ [ 796, 817 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T27" } ] }, { "id": "8323299_E16", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "partial glycosylation" ], "offsets": [ [ 796, 817 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8323299_T8" }, { "role": "Site", "ref_id": "8323299_T29" } ] } ]

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[ { "id": "7650037__text", "type": "abstract", "text": [ "Hydroxyarginine-containing polyphenolic proteins in the adhesive plaques of the marine mussel Mytilus edulis. \nAn unusual polymorphic protein family of nine or more variants has been isolated from the byssal adhesive plaques and foot of the marine mussel Mytilus edulis. In accordance with established terminology, the family is referred to as M. edulis foot protein 3 or simply Mefp-3. Variants of Mefp-3 have molecular masses of about 6 kDa, isoelectric points greater than 10.5, and an amino acid composition dominated by six amino acids: glycine, asparagine, 3,4-dihydroxyphenylalanine (Dopa), tryptophan, arginine, and an unknown basic amino acid. The latter has been isolated and identified as 4-hydroxyarginine using fast atom bombardment mass spectrometry and appropriate standards. The primary structure of variant Mefp-3F has been determined by peptide mapping using automated Edman sequencing in combination with fast atom bombardment and matrix-assisted laser desorption ionization mass spectrometry: ADYYGPNYGPPRRYGGGNYNRYNRYGRRYGGYKGWNNGWNRGRRGKYW where Y represents Dopa, and R represents hydroxyarginine. Notably, the 4 occurrences of RY are marked by a resistance to trypsin digestion. Although the conversion of tyrosines to Dopa is essentially complete, hydroxylation of arginines varies between 40 and 80%. In contrast to other mussel adhesive proteins such as Mefp-1 and -2 which have large numbers of highly conserved, tandemly repeated peptide motifs, Mefp-3 has only short sporadic repeats. The specific function of Mefp-3 in byssal adhesion is unknown. " ], "offsets": [ [ 0, 1578 ] ] } ]

[ { "id": "7650037_T1", "type": "Protein", "text": [ " Mefp-3" ], "offsets": [ [ 378, 385 ] ], "normalized": [] }, { "id": "7650037_T2", "type": "Protein", "text": [ "Mefp-3" ], "offsets": [ [ 399, 405 ] ], "normalized": [] }, { "id": "7650037_T3", "type": "Protein", "text": [ "Mefp-3F" ], "offsets": [ [ 824, 831 ] ], "normalized": [] }, { "id": "7650037_T4", "type": "Protein", "text": [ "Mefp-1" ], "offsets": [ [ 1381, 1387 ] ], "normalized": [] }, { "id": "7650037_T5", "type": "Protein", "text": [ "-2" ], "offsets": [ [ 1392, 1394 ] ], "normalized": [] }, { "id": "7650037_T6", "type": "Protein", "text": [ "Mefp-3" ], "offsets": [ [ 1475, 1481 ] ], "normalized": [] }, { "id": "7650037_T7", "type": "Protein", "text": [ "Mefp-3" ], "offsets": [ [ 1540, 1546 ] ], "normalized": [] }, { "id": "7650037_T9", "type": "Entity", "text": [ "tyrosines" ], "offsets": [ [ 1230, 1239 ] ], "normalized": [] }, { "id": "7650037_T11", "type": "Entity", "text": [ "arginines" ], "offsets": [ [ 1290, 1299 ] ], "normalized": [] } ]

[ { "id": "7650037_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "conversion" ], "offsets": [ [ 1216, 1226 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7650037_T3" }, { "role": "Site", "ref_id": "7650037_T9" } ] }, { "id": "7650037_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1273, 1286 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7650037_T3" }, { "role": "Site", "ref_id": "7650037_T11" } ] } ]

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[ { "id": "12763018__text", "type": "abstract", "text": [ "Lysine hydroxylation of collagen in a fibroblast cell culture system. \nThe lysine (Lys) hydroxylation pattern of type I collagen produced by human fibroblasts in culture was analyzed and compared. Fibroblasts were cultured from normal human skin (NSF), keloid (KDF), fetal skin (FDF), and skin tissues of Ehlers-Danlos syndrome type VIA and VIB patients (EDS-VIA and -VIB). The type I collagen alpha chains with or without non-helical telopeptides were purified from the insoluble matrix and analyzed. In comparison with NSFs, KDF and FDF showed significantly higher Lys hydroxylation, particularly in the telopeptide domains of both alpha chains. Both EDS-VIA and -VIB showed markedly lower Lys hydroxylation in the helical domains of both alpha chains whereas that in the telopeptides was comparable with those of NSFs. A similar profile was observed in the tissue sample of the EDS-VIB patient. These results demonstrate that the Lys hydroxylation pattern is domain-specific within the collagen molecule and that this method is useful to characterize the cell phenotypes in normal/pathological connective tissues. " ], "offsets": [ [ 0, 1117 ] ] } ]

[ { "id": "12763018_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 24, 32 ] ], "normalized": [] }, { "id": "12763018_T2", "type": "Protein", "text": [ "type I collagen" ], "offsets": [ [ 113, 128 ] ], "normalized": [] }, { "id": "12763018_T3", "type": "Protein", "text": [ "type I collagen alpha chains" ], "offsets": [ [ 378, 406 ] ], "normalized": [] }, { "id": "12763018_T4", "type": "Protein", "text": [ "alpha chains" ], "offsets": [ [ 634, 646 ] ], "normalized": [] }, { "id": "12763018_T5", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 989, 997 ] ], "normalized": [] }, { "id": "12763018_T6", "type": "Entity", "text": [ "Lysine" ], "offsets": [ [ 0, 6 ] ], "normalized": [] }, { "id": "12763018_T8", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 75, 81 ] ], "normalized": [] }, { "id": "12763018_T9", "type": "Entity", "text": [ "Lys" ], "offsets": [ [ 83, 86 ] ], "normalized": [] }, { "id": "12763018_T11", "type": "Entity", "text": [ "Lys" ], "offsets": [ [ 567, 570 ] ], "normalized": [] }, { "id": "12763018_T13", "type": "Entity", "text": [ "Lys" ], "offsets": [ [ 933, 936 ] ], "normalized": [] } ]

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[ { "id": "3366244__text", "type": "abstract", "text": [ "Isolation and identification of hydroxyproline analogues of bradykinin in human urine. \nHydroxyproline (Hyp) analogues of bradykinin and lysyl-bradykinin, in which the third residue of bradykinin, proline, is replaced by hydroxyproline, were isolated from human urine. Their amino acid sequences were confirmed by both amino acid and sequence analyses, and also by comparison of their chromatographic behavior with that of synthetic peptides. The possibility that Lys-Ala3-bradykinin, isolated by Mindroiu et al. [(1986) J. Biol. Chem. 261, 7407-7411] from human urine, was actually Lys-Hyp3-bradykinin is discussed. " ], "offsets": [ [ 0, 617 ] ] } ]

[ { "id": "3366244_T1", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 60, 70 ] ], "normalized": [] }, { "id": "3366244_T2", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 122, 132 ] ], "normalized": [] }, { "id": "3366244_T3", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 185, 195 ] ], "normalized": [] }, { "id": "3366244_T4", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 473, 483 ] ], "normalized": [] }, { "id": "3366244_T5", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 592, 602 ] ], "normalized": [] }, { "id": "3366244_T6", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 197, 204 ] ], "normalized": [] } ]

[ { "id": "3366244_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "replaced by hydroxyproline" ], "offsets": [ [ 209, 235 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3366244_T3" }, { "role": "Site", "ref_id": "3366244_T6" } ] } ]

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[ { "id": "6203908__text", "type": "abstract", "text": [ "Primary structure of human alpha 2-macroglobulin. V. The complete structure. \nThe primary structure of the tetrameric plasma glycoprotein human alpha 2-macroglobulin has been determined. The identical subunits contain 1451 amino acid residues. Glucosamine-based oligosaccharide groups are attached to asparagine residues 32, 47, 224, 373, 387, 846, 968, and 1401. Eleven intrachain disulfide bridges have been placed (Cys25-Cys63, Cys228-Cys276, Cys246-Cys264, Cys255-Cys408, Cys572-Cys748, Cys619-Cys666, Cys798-Cys826, Cys824-Cys860, Cys898-Cys1298, Cys1056-Cys1104, and Cys1329-Cys1444). Cys-447 probably forms an interchain bridge with Cys-447 from another subunit. The beta-SH group of Cys-949 is thiol esterified to the gamma-carbonyl group of Glx-952, thus forming an activatable reactive site which can mediate covalent binding of nucleophiles. A putative transglutaminase cross-linking site is constituted by Gln-670 and Gln-671. The primary sites of proteolytic cleavage in the activation cleavage area (the \"bait\" region) are located in the sequence: -Arg681-Val-Gly-Phe-Tyr-Glu-. The molecular weight of the unmodified alpha 2-macroglobulin subunit is 160,837 and approximately 179,000, including the carbohydrate groups. The presence of possible internal homologies within the alpha 2-macroglobulin subunit is discussed. A comparison of stretches of sequences from alpha 2-macroglobulin with partial sequence data for complement components C3 and C4 indicates that these proteins are evolutionary related. The properties of alpha 2-macroglobulin are discussed within the context of proteolytically regulated systems with particular reference to the complement components C3 and C4. " ], "offsets": [ [ 0, 1695 ] ] } ]

[ { "id": "6203908_T1", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 27, 48 ] ], "normalized": [] }, { "id": "6203908_T2", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 144, 165 ] ], "normalized": [] }, { "id": "6203908_T3", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 1131, 1152 ] ], "normalized": [] }, { "id": "6203908_T4", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 1290, 1311 ] ], "normalized": [] }, { "id": "6203908_T5", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 1378, 1399 ] ], "normalized": [] }, { "id": "6203908_T6", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 1537, 1558 ] ], "normalized": [] }, { "id": "6203908_T8", "type": "Entity", "text": [ "asparagine residues 32" ], "offsets": [ [ 301, 323 ] ], "normalized": [] }, { "id": "6203908_T9", "type": "Entity", "text": [ "47" ], "offsets": [ [ 325, 327 ] ], "normalized": [] }, { "id": "6203908_T10", "type": "Entity", "text": [ "224" ], "offsets": [ [ 329, 332 ] ], "normalized": [] }, { "id": "6203908_T11", "type": "Entity", "text": [ "373" ], "offsets": [ [ 334, 337 ] ], "normalized": [] }, { "id": "6203908_T12", "type": "Entity", "text": [ "387" ], "offsets": [ [ 339, 342 ] ], "normalized": [] }, { "id": "6203908_T13", "type": "Entity", "text": [ "846" ], "offsets": [ [ 344, 347 ] ], "normalized": [] }, { "id": "6203908_T14", "type": "Entity", "text": [ "968" ], "offsets": [ [ 349, 352 ] ], "normalized": [] }, { "id": "6203908_T15", "type": "Entity", "text": [ "1401" ], "offsets": [ [ 358, 362 ] ], "normalized": [] } ]

[ { "id": "6203908_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glucosamine-based oligosaccharide groups are attached" ], "offsets": [ [ 244, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6203908_T2" }, { "role": "Site", "ref_id": "6203908_T14" } ] }, { "id": "6203908_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glucosamine-based oligosaccharide groups are attached" ], "offsets": [ [ 244, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6203908_T2" }, { "role": "Site", "ref_id": "6203908_T13" } ] }, { "id": "6203908_E3", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glucosamine-based oligosaccharide groups are attached" ], "offsets": [ [ 244, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6203908_T2" }, { "role": "Site", "ref_id": "6203908_T8" } ] }, { "id": "6203908_E4", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glucosamine-based oligosaccharide groups are attached" ], "offsets": [ [ 244, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6203908_T2" }, { "role": "Site", "ref_id": "6203908_T15" } ] }, { "id": "6203908_E5", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glucosamine-based oligosaccharide groups are attached" ], "offsets": [ [ 244, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6203908_T2" }, { "role": "Site", "ref_id": "6203908_T9" } ] }, { "id": "6203908_E6", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glucosamine-based oligosaccharide groups are attached" ], "offsets": [ [ 244, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6203908_T2" }, { "role": "Site", "ref_id": "6203908_T12" } ] }, { "id": "6203908_E7", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glucosamine-based oligosaccharide groups are attached" ], "offsets": [ [ 244, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6203908_T2" }, { "role": "Site", "ref_id": "6203908_T11" } ] }, { "id": "6203908_E8", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "Glucosamine-based oligosaccharide groups are attached" ], "offsets": [ [ 244, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6203908_T2" }, { "role": "Site", "ref_id": "6203908_T10" } ] } ]

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[ { "id": "11356363__text", "type": "abstract", "text": [ "Re-SET-ting heterochromatin by histone methyltransferases. \nHistone methylation was first described more than 35 years ago, but its role has remained enigmatic. Proposed functions range from transcriptional regulation to the higher-order packaging of chromatin in preparation for mitotic condensation. Histone methylation can occur on Arg or Lys residues, with an exquisite site selectivity for Lys methylation at specific positions in the N-termini of histones H3 and H4. Thus, Lys methylation joins acetylation and phosphorylation as a third component of a 'histone code' that modifies the underlying chromatin structure of the genetic information. Notably, in contrast to acetylation and phosphorylation, Lys methylation appears to be a relatively stable histone modification, thereby providing an ideal epigenetic mark for more long-term maintenance of chromatin states. The recent discovery of the first histone Lys methyltransferase has allowed the identification of a molecular mechanism in which the specific methylation of histone H3 at Lys9 generates a binding site for heterochromatin-associated proteins. These findings have broad implications for the overall functional organization of chromosome structure at constitutive heterochromatin (e.g. centromeres) and for chromatin-dependent inheritance of gene expression patterns. This review discusses how understanding this methylation system should address some of the long-standing mysteries of heterochromatin. " ], "offsets": [ [ 0, 1475 ] ] } ]

[ { "id": "11356363_T1", "type": "Protein", "text": [ "histones H3" ], "offsets": [ [ 453, 464 ] ], "normalized": [] }, { "id": "11356363_T2", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 469, 471 ] ], "normalized": [] }, { "id": "11356363_T3", "type": "Protein", "text": [ "histone H3" ], "offsets": [ [ 1032, 1042 ] ], "normalized": [] }, { "id": "11356363_T4", "type": "Entity", "text": [ "Histone" ], "offsets": [ [ 60, 67 ] ], "normalized": [] }, { "id": "11356363_T6", "type": "Entity", "text": [ "Lys" ], "offsets": [ [ 395, 398 ] ], "normalized": [] }, { "id": "11356363_T8", "type": "Entity", "text": [ "Lys" ], "offsets": [ [ 479, 482 ] ], "normalized": [] }, { "id": "11356363_T11", "type": "Entity", "text": [ "Lys9" ], "offsets": [ [ 1046, 1050 ] ], "normalized": [] } ]

[ { "id": "11356363_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 68, 79 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "11356363_T4" } ] }, { "id": "11356363_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 399, 410 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "11356363_T1" }, { "role": "Site", "ref_id": "11356363_T6" } ] }, { "id": "11356363_E3", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 399, 410 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "11356363_T2" }, { "role": "Site", "ref_id": "11356363_T6" } ] }, { "id": "11356363_E4", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 483, 494 ] ] }, "arguments": [ { "role": "Site", "ref_id": "11356363_T8" } ] }, { "id": "11356363_E5", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1017, 1028 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "11356363_T3" }, { "role": "Site", "ref_id": "11356363_T11" } ] } ]

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[ { "id": "12029842__text", "type": "abstract", "text": [ "Lysine hydroxylation and crosslinking of collagen. \n" ], "offsets": [ [ 0, 52 ] ] } ]

[ { "id": "12029842_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 41, 49 ] ], "normalized": [] }, { "id": "12029842_T2", "type": "Entity", "text": [ "Lysine" ], "offsets": [ [ 0, 6 ] ], "normalized": [] } ]

[ { "id": "12029842_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 7, 20 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "12029842_T1" }, { "role": "Site", "ref_id": "12029842_T2" } ] } ]

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[ { "id": "6402709__text", "type": "abstract", "text": [ "Structure of the serine chemoreceptor in Escherichia coli. \nMany biological processes depend on the function of proteins that detect changes in a cell's environment and transmit the information to the cytoplasm, for example, peptide hormone receptors. In Escherichia coli this class of proteins is exemplified by the sensory transducers (also called signalling proteins or methyl-accepting chemotaxis proteins) which have a central role in mediating chemotactic behaviour. The sensory transducers are the products of four genes: tsr, tar, tap and trg. Each transducer detects changes in the environmental concentration of one or a very few attractants: Tsr, serine; Tar, aspartate and maltose; Tap, unknown; and Trg, ribose and galactose. Tsr and Tar act directly as chemoreceptors for the amino acid attractants and signal changes in their degree of occupancy to the flagellar apparatus. Detection of these changes in occupancy is made possible as the transducers are methylated at multiple glutamate residues such that their level of methylation reflects the most recent chemoeffector concentration. Biochemical and genetic information concerning the serine transducer protein has been accumulating rapidly but little is known about the structure of the molecule. We present here the nucleotide sequence of the tsr gene of E. coli; the amino acid sequence derived from it suggests that the Tsr transducer protein has a relatively simple transmembrane structure that may place limits on the mechanisms available for the transmission of sensory information into the cell. " ], "offsets": [ [ 0, 1579 ] ] } ]

[ { "id": "6402709_T1", "type": "Protein", "text": [ "tsr" ], "offsets": [ [ 531, 534 ] ], "normalized": [] }, { "id": "6402709_T2", "type": "Protein", "text": [ "tar" ], "offsets": [ [ 536, 539 ] ], "normalized": [] }, { "id": "6402709_T3", "type": "Protein", "text": [ "tap" ], "offsets": [ [ 541, 544 ] ], "normalized": [] }, { "id": "6402709_T4", "type": "Protein", "text": [ "trg" ], "offsets": [ [ 549, 552 ] ], "normalized": [] }, { "id": "6402709_T5", "type": "Protein", "text": [ "Tsr" ], "offsets": [ [ 656, 659 ] ], "normalized": [] }, { "id": "6402709_T6", "type": "Protein", "text": [ "Tar" ], "offsets": [ [ 669, 672 ] ], "normalized": [] }, { "id": "6402709_T7", "type": "Protein", "text": [ "Tap" ], "offsets": [ [ 697, 700 ] ], "normalized": [] }, { "id": "6402709_T8", "type": "Protein", "text": [ "Trg" ], "offsets": [ [ 715, 718 ] ], "normalized": [] }, { "id": "6402709_T9", "type": "Protein", "text": [ "Tsr" ], "offsets": [ [ 743, 746 ] ], "normalized": [] }, { "id": "6402709_T10", "type": "Protein", "text": [ "Tar" ], "offsets": [ [ 751, 754 ] ], "normalized": [] }, { "id": "6402709_T11", "type": "Protein", "text": [ "Tsr" ], "offsets": [ [ 1399, 1402 ] ], "normalized": [] }, { "id": "6402709_T13", "type": "Entity", "text": [ "multiple glutamate residues" ], "offsets": [ [ 988, 1015 ] ], "normalized": [] } ]

[ { "id": "6402709_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 974, 984 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6402709_T1" }, { "role": "Site", "ref_id": "6402709_T13" } ] }, { "id": "6402709_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 974, 984 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6402709_T2" }, { "role": "Site", "ref_id": "6402709_T13" } ] }, { "id": "6402709_E3", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 974, 984 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6402709_T4" }, { "role": "Site", "ref_id": "6402709_T13" } ] }, { "id": "6402709_E4", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 974, 984 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6402709_T3" }, { "role": "Site", "ref_id": "6402709_T13" } ] } ]

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[ { "id": "7607314__text", "type": "abstract", "text": [ "Multiplicity of N-terminal structures of medium-chain alcohol dehydrogenases. Mass-spectrometric analysis of plant, lower vertebrate and higher vertebrate class I, II, and III forms of the enzyme. \nTen different alcohol dehydrogenases, representing several classes of the enzyme and a wide spread of organisms, were analyzed for patterns of N-terminal structures utilizing a combination of conventional and mass spectrometric peptide analysis. Results show all forms to be N-terminally acetylated and allow comparisons of now 40 such alcohol dehydrogenases covering a large span of forms and origins. Patterns illustrate roles of acetylation in proteins in general, define special importance of the class I N-terminal acetylation, and distinguish separate acetylated structures for all classes, as well as a common alcohol dehydrogenase motif. " ], "offsets": [ [ 0, 844 ] ] } ]

[ { "id": "7607314_T1", "type": "Protein", "text": [ "medium-chain alcohol dehydrogenases" ], "offsets": [ [ 41, 76 ] ], "normalized": [] }, { "id": "7607314_T2", "type": "Entity", "text": [ "N-terminally" ], "offsets": [ [ 473, 485 ] ], "normalized": [] }, { "id": "7607314_T4", "type": "Entity", "text": [ "N-terminal" ], "offsets": [ [ 707, 717 ] ], "normalized": [] } ]

[ { "id": "7607314_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 486, 496 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7607314_T1" }, { "role": "Site", "ref_id": "7607314_T2" } ] }, { "id": "7607314_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 718, 729 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7607314_T1" }, { "role": "Site", "ref_id": "7607314_T4" } ] } ]

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[ { "id": "2049076__text", "type": "abstract", "text": [ "Natural human interferon-alpha 2 is O-glycosylated. \nNatural human interferon alpha 2 (IFN-alpha 2) was isolated from a preparation of partially purified human leucocyte IFN by monoclonal-antibody immunoaffinity chromatography. The purified protein had a specific activity of 1.5 x 10(8) i.u./mg; it was estimated to constitute 10-20% of the total antiviral activity of leucocyte IFN. N-Terminal amino-acid-sequence analysis identified the subspecies IFN-alpha 2b and/or IFN-alpha 2c, whereas IFN-alpha 2a was not detectable. The structure of natural IFN-alpha 2 was found to differ from that of its recombinant (Escherichia coli-derived) equivalent. First, reverse-phase h.p.l.c. showed that natural IFN-alpha 2 was significantly more hydrophilic then expected. Secondly, the apparent molecular mass of the natural protein determined by SDS/PAGE was higher than that of recombinant IFN-alpha 2; incubation under mild alkaline conditions known to eliminate O-linked carbohydrates resulted in a reduction of the apparent molecular mass to that of the recombinant protein. On sequence analysis of proteolytic peptides, Thr-106 was found to be modified. These results suggested that Thr-106 of natural IFN-alpha 2 carries O-linked carbohydrates. Reverse-phase h.p.l.c. as well as SDS/PAGE of natural IFN-alpha 2 showed that glycosylation is heterogeneous. For characterization of the carbohydrate moieties, the protein was treated with neuraminidase and/or O-glycanase and analysed by gel electrophoresis; in addition, glycopeptides obtained by proteinase digestion and separated by h.p.l.c. were characterized by sequence analysis and m.s. Further information on the composition of the glycans was obtained by monosaccharide analysis. The results indicate that natural IFN-alpha 2 contains the disaccharide galactosyl-N-acetylgalactosamine (Gal-GalNAc) linked to Thr-106. In part of the molecules, this core carbohydrate carries (alpha-)N-acetylneuraminic acid, whereas a disaccharide, probably N-acetyl-lactosamine, is bound to Gal-GalNAc in another proportion of the protein. Further glycosylation isomers are present in small amounts. As IFN-alpha 2 is the only IFN-alpha species with a threonine residue at position 106, it may represent the only O-glycosylated human IFN-alpha protein. " ], "offsets": [ [ 0, 2289 ] ] } ]

[ { "id": "2049076_T1", "type": "Protein", "text": [ "interferon-alpha 2" ], "offsets": [ [ 14, 32 ] ], "normalized": [] }, { "id": "2049076_T2", "type": "Protein", "text": [ "interferon alpha 2" ], "offsets": [ [ 67, 85 ] ], "normalized": [] }, { "id": "2049076_T3", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 87, 98 ] ], "normalized": [] }, { "id": "2049076_T4", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 451, 462 ] ], "normalized": [] }, { "id": "2049076_T5", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 471, 482 ] ], "normalized": [] }, { "id": "2049076_T6", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 493, 504 ] ], "normalized": [] }, { "id": "2049076_T7", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 551, 562 ] ], "normalized": [] }, { "id": "2049076_T8", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 701, 712 ] ], "normalized": [] }, { "id": "2049076_T9", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 883, 894 ] ], "normalized": [] }, { "id": "2049076_T10", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 1199, 1210 ] ], "normalized": [] }, { "id": "2049076_T11", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 1297, 1308 ] ], "normalized": [] }, { "id": "2049076_T12", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 1767, 1778 ] ], "normalized": [] }, { "id": "2049076_T13", "type": "Protein", "text": [ "IFN-alpha 2" ], "offsets": [ [ 2139, 2150 ] ], "normalized": [] }, { "id": "2049076_T14", "type": "Entity", "text": [ "Thr-106" ], "offsets": [ [ 1180, 1187 ] ], "normalized": [] }, { "id": "2049076_T17", "type": "Entity", "text": [ "threonine residue" ], "offsets": [ [ 2188, 2205 ] ], "normalized": [] } ]

[ { "id": "2049076_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carries O-linked carbohydrates" ], "offsets": [ [ 1211, 1241 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2049076_T10" }, { "role": "Site", "ref_id": "2049076_T14" } ] }, { "id": "2049076_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 1321, 1334 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2049076_T11" } ] }, { "id": "2049076_E3", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "O-glycosylated" ], "offsets": [ [ 2249, 2263 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2049076_T13" }, { "role": "Site", "ref_id": "2049076_T17" } ] } ]

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[ { "id": "7021545__text", "type": "abstract", "text": [ "The amino acid sequence of elongation factor Tu of Escherichia coli. The complete sequence. \nThe complete amino acid sequence of elongation factor Tu of Escherichia coli has been established by sequencing overlapping cyanogen bromide and tryptic peptides. Sequence analysis of peptides was done primarily by solid-phase Edman degradation. elongation factor Tu is a single chain polypeptide composed of 393 amino acids (Mr = 43,225). Its NH2 terminus is blocked with an acetyl group, as determined by mass spectroscopy, and lysine 56 is partially methylated. The cysteine residues associated with aminoacyl tRNA and guanosine nucleotide binding are located at positions 81 and 137, respectively. Although elongation factor Tu is coded for by two genes, the only site of microheterogeneity found was at the carboxyl terminus (residue 393), which is either glycine or serine. Comparison of the first 140 amino acids of elongation factor Tu and of elongation factor Tu shows a strong (31%) sequence homology. In addition, secondary structure calculations predict remarkable conformational similarities between the two proteins. The NH2-terminal region of elongation factor Tu appears to be composed of two beta-sheet domains connected by an exposed, alpha-helical bridge, which includes a 14-amino acid segment released by limited treatment with trypsin. Structural features of the aminoacyl-tRNA binding site are discussed in the light of sequence and other chemical and biochemical data. " ], "offsets": [ [ 0, 1496 ] ] } ]

[ { "id": "7021545_T1", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 27, 47 ] ], "normalized": [] }, { "id": "7021545_T2", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 130, 150 ] ], "normalized": [] }, { "id": "7021545_T3", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 342, 362 ] ], "normalized": [] }, { "id": "7021545_T4", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 710, 730 ] ], "normalized": [] }, { "id": "7021545_T5", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 923, 943 ] ], "normalized": [] }, { "id": "7021545_T6", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 951, 971 ] ], "normalized": [] }, { "id": "7021545_T7", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 1160, 1180 ] ], "normalized": [] }, { "id": "7021545_T8", "type": "Entity", "text": [ "lysine 56" ], "offsets": [ [ 527, 536 ] ], "normalized": [] } ]

[ { "id": "7021545_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 550, 560 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7021545_T3" }, { "role": "Site", "ref_id": "7021545_T8" } ] } ]

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[ { "id": "2187868__text", "type": "abstract", "text": [ "Partial purification and characterization of bovine liver aspartyl beta-hydroxylase. \nIn vitro hydroxylation of aspartic acid has recently been demonstrated in a synthetic peptide based on the structure of the first epidermal growth factor domain in human factor IX (Gronke, R. S., VanDusen, W. J., Garsky, V. M., Jacobs, J. W., Sardana, M. K., Stern, A. M., and Friedman, P. A. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 3609-3613). The putative enzyme responsible for the posttranslational modification, aspartyl beta-hydroxylase, has been shown to be a member of a class of 2-ketoglutarate-dependent dioxygenases, which include prolyl-4- and lysyl-hydroxylases. In the present study, we describe the solubilization with nonionic detergent of the enzyme from bovine liver microsomes and its purification using DEAE-cellulose followed by heparin-Sepharose. No additional detergent was required during purification. The partially purified enzyme preparation was found to contain no prolyl-4- or lysyl-hydroxylase activity. Using a synthetic peptide based on the structure of the epidermal growth factor-like region in human factor X as substrate, the apparent Km values for iron and alpha-ketoglutarate were 3 and 5 microM, respectively. The enzyme hydroxylated the factor X peptide with the same stereospecificity (erythro beta-hydroxyaspartic acid) and occurred only at the aspartate corresponding to the position seen in vivo. Furthermore, the extent to which either peptide (factor IX or X) was hydroxylated reflected the extent of hydroxylation observed for both human plasma factors IX and X. " ], "offsets": [ [ 0, 1597 ] ] } ]

[ { "id": "2187868_T1", "type": "Protein", "text": [ "aspartyl beta-hydroxylase" ], "offsets": [ [ 58, 83 ] ], "normalized": [] }, { "id": "2187868_T2", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 256, 265 ] ], "normalized": [] }, { "id": "2187868_T3", "type": "Protein", "text": [ "aspartyl beta-hydroxylase" ], "offsets": [ [ 504, 529 ] ], "normalized": [] }, { "id": "2187868_T4", "type": "Protein", "text": [ "factor X" ], "offsets": [ [ 1122, 1130 ] ], "normalized": [] }, { "id": "2187868_T5", "type": "Protein", "text": [ "factor X" ], "offsets": [ [ 1264, 1272 ] ], "normalized": [] }, { "id": "2187868_T6", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 1477, 1486 ] ], "normalized": [] }, { "id": "2187868_T7", "type": "Protein", "text": [ "X" ], "offsets": [ [ 1490, 1491 ] ], "normalized": [] }, { "id": "2187868_T8", "type": "Protein", "text": [ "factors IX" ], "offsets": [ [ 1579, 1589 ] ], "normalized": [] }, { "id": "2187868_T9", "type": "Protein", "text": [ "X" ], "offsets": [ [ 1594, 1595 ] ], "normalized": [] }, { "id": "2187868_T11", "type": "Entity", "text": [ "aspartic acid" ], "offsets": [ [ 112, 125 ] ], "normalized": [] }, { "id": "2187868_T13", "type": "Entity", "text": [ "aspartate" ], "offsets": [ [ 1374, 1383 ] ], "normalized": [] } ]

[ { "id": "2187868_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 95, 108 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2187868_T2" }, { "role": "Site", "ref_id": "2187868_T11" } ] }, { "id": "2187868_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 1247, 1259 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2187868_T5" }, { "role": "Site", "ref_id": "2187868_T13" } ] }, { "id": "2187868_E3", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 1497, 1509 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2187868_T7" } ] }, { "id": "2187868_E4", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 1497, 1509 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2187868_T6" } ] }, { "id": "2187868_E5", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1534, 1547 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2187868_T9" } ] }, { "id": "2187868_E6", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1534, 1547 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2187868_T8" } ] } ]

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[ { "id": "3115194__text", "type": "abstract", "text": [ "Collagen biosynthesis and isomorphism in a case of Ehlers-Danlos syndrome type VI. \nCollagen metabolism was studied in fibroblasts grown from a skin biopsy specimen of a patient who presented the striking clinical features of Ehlers-Danlos syndrome and, in particular, hyperextensibility of the skin, hypermobility of the joints, and kyphoscoliosis. A reduction in lysine hydroxylation, characteristic of Ehlers-Danlos Type VI, was observed after labelling of the collagen with 14C-proline and 3H-lysine. Other modifications in the collagen metabolism of fibroblast cultures were noted, including an increase in collagen and total protein synthesis, and an increase in both the Type I and Type III collagen. The percentage of Type III collagen was, however, lower than in the control fibroblasts. The results point out the complexity of collagen disturbances in Ehlers-Danlos Type VI. " ], "offsets": [ [ 0, 885 ] ] } ]

[ { "id": "3115194_T1", "type": "Protein", "text": [ "Collagen" ], "offsets": [ [ 0, 8 ] ], "normalized": [] }, { "id": "3115194_T2", "type": "Protein", "text": [ "Collagen" ], "offsets": [ [ 84, 92 ] ], "normalized": [] }, { "id": "3115194_T3", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 464, 472 ] ], "normalized": [] }, { "id": "3115194_T4", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 532, 540 ] ], "normalized": [] }, { "id": "3115194_T5", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 612, 620 ] ], "normalized": [] }, { "id": "3115194_T6", "type": "Protein", "text": [ "Type I" ], "offsets": [ [ 678, 684 ] ], "normalized": [] }, { "id": "3115194_T7", "type": "Protein", "text": [ "Type III collagen" ], "offsets": [ [ 689, 706 ] ], "normalized": [] }, { "id": "3115194_T8", "type": "Protein", "text": [ "Type III collagen" ], "offsets": [ [ 726, 743 ] ], "normalized": [] }, { "id": "3115194_T9", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 365, 371 ] ], "normalized": [] } ]

[ { "id": "3115194_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 372, 385 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3115194_T3" }, { "role": "Site", "ref_id": "3115194_T9" } ] } ]

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[ { "id": "2492106__text", "type": "abstract", "text": [ "Hydroxylation of aspartic acid in domains homologous to the epidermal growth factor precursor is catalyzed by a 2-oxoglutarate-dependent dioxygenase. \n3-Hydroxyaspartic acid and 3-hydroxyasparagine are two rare amino acids that are present in domains homologous to the epidermal growth factor precursor in vitamin K-dependent plasma proteins as well as in proteins that do not require vitamin K for normal biosynthesis. They are formed by posttranslational hydroxylation of aspartic acid and asparagine, respectively. The first epidermal growth factor-like domain in factor IX (residues 45-87) was synthesized with aspartic acid in position 64, replacing 3-hydroxyaspartic acid. It was used as substrate in a hydroxylase assay with rat liver microsomes as the source of enzyme and reaction conditions that satisfy the requirements of 2-oxoglutarate-dependent dioxygenases. The synthetic peptide stimulated the 2-oxoglutarate decarboxylation in contrast to synthetic, modified epidermal growth factor (Met-21 and His-22 deleted and Glu-24 replaced by Asp) and synthetic peptides corresponding to residues 60-71 in human factor IX. This indicates that the hydroxylase is a 2-oxoglutarate-dependent dioxygenase with a selective substrate requirement. " ], "offsets": [ [ 0, 1248 ] ] } ]

[ { "id": "2492106_T1", "type": "Protein", "text": [ "epidermal growth factor precursor" ], "offsets": [ [ 60, 93 ] ], "normalized": [] }, { "id": "2492106_T2", "type": "Protein", "text": [ "2-oxoglutarate-dependent dioxygenase" ], "offsets": [ [ 112, 148 ] ], "normalized": [] }, { "id": "2492106_T3", "type": "Protein", "text": [ "epidermal growth factor precursor" ], "offsets": [ [ 269, 302 ] ], "normalized": [] }, { "id": "2492106_T4", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 567, 576 ] ], "normalized": [] }, { "id": "2492106_T5", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 1119, 1128 ] ], "normalized": [] }, { "id": "2492106_T7", "type": "Entity", "text": [ "aspartic acid" ], "offsets": [ [ 17, 30 ] ], "normalized": [] }, { "id": "2492106_T10", "type": "Entity", "text": [ "aspartic acid" ], "offsets": [ [ 474, 487 ] ], "normalized": [] }, { "id": "2492106_T11", "type": "Entity", "text": [ "asparagine" ], "offsets": [ [ 492, 502 ] ], "normalized": [] } ]

[ { "id": "2492106_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "Hydroxylation" ], "offsets": [ [ 0, 13 ] ] }, "arguments": [ { "role": "Site", "ref_id": "2492106_T7" } ] }, { "id": "2492106_E2", "type": "Positive_regulation", "trigger": { "text": [ "catalyzed" ], "offsets": [ [ 97, 106 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2492106_E1" }, { "role": "Cause", "ref_id": "2492106_T2" } ] }, { "id": "2492106_E3", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 457, 470 ] ] }, "arguments": [ { "role": "Site", "ref_id": "2492106_T11" } ] }, { "id": "2492106_E4", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 457, 470 ] ] }, "arguments": [ { "role": "Site", "ref_id": "2492106_T10" } ] } ]

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[ { "id": "4994464__text", "type": "abstract", "text": [ "Localization of methylated arginine in the A1 protein from myelin. \nMethylated arginine residues are found at only one site (position 107) of the polypeptide chain of the A1 protein, as shown by analysis of tryptic and peptic peptides; these analyses show 0.2 mole of N(G)-dimethylarginine and 0.4-0.8 mole of N(G)-monomethylarginine per mole of A1 protein. " ], "offsets": [ [ 0, 358 ] ] } ]

[ { "id": "4994464_T1", "type": "Protein", "text": [ "A1 protein" ], "offsets": [ [ 43, 53 ] ], "normalized": [] }, { "id": "4994464_T2", "type": "Protein", "text": [ "myelin" ], "offsets": [ [ 59, 65 ] ], "normalized": [] }, { "id": "4994464_T3", "type": "Protein", "text": [ "A1 protein" ], "offsets": [ [ 171, 181 ] ], "normalized": [] }, { "id": "4994464_T4", "type": "Entity", "text": [ "arginine" ], "offsets": [ [ 27, 35 ] ], "normalized": [] }, { "id": "4994464_T6", "type": "Entity", "text": [ "arginine" ], "offsets": [ [ 79, 87 ] ], "normalized": [] }, { "id": "4994464_T7", "type": "Entity", "text": [ "A1 protein" ], "offsets": [ [ 171, 181 ] ], "normalized": [] } ]

[ { "id": "4994464_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "Methylated" ], "offsets": [ [ 68, 78 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4994464_T3" }, { "role": "Site", "ref_id": "4994464_T6" } ] } ]

[ { "id": "4994464_1", "entity_ids": [ "4994464_T2", "4994464_T1" ] } ]

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[ { "id": "6262305__text", "type": "abstract", "text": [ "The complete amino acid sequence of bovine heart cytochrome oxidase subunit VI. \nThe amino acid sequence of subunit VI derived from bovine heart cytochrome oxidase has been completed and is a single polypeptide chain consisting of 85 amino acid residues. The sequence is: acetyl (formula: see text). The NH2 terminus of subunit VI is blocked with an acetyl group and the molecular weight of the native protein including the acetyl group is 10,067. From the sequence of subunit VI, it is obvious that this subunit corresponds to polypeptide VII of Steffens et al. (Steffens, G. C. M., Steffens, G. J., and Buse, G. (1979) Hoppe-Seyler's Z. Physiol. Chem. 360, 1641-1650). " ], "offsets": [ [ 0, 671 ] ] } ]

[ { "id": "6262305_T1", "type": "Protein", "text": [ "cytochrome oxidase subunit VI" ], "offsets": [ [ 49, 78 ] ], "normalized": [] }, { "id": "6262305_T2", "type": "Protein", "text": [ "subunit VI" ], "offsets": [ [ 108, 118 ] ], "normalized": [] }, { "id": "6262305_T3", "type": "Protein", "text": [ "subunit VI" ], "offsets": [ [ 320, 330 ] ], "normalized": [] }, { "id": "6262305_T4", "type": "Protein", "text": [ "subunit VI" ], "offsets": [ [ 469, 479 ] ], "normalized": [] }, { "id": "6262305_T5", "type": "Entity", "text": [ "NH2 terminus" ], "offsets": [ [ 304, 316 ] ], "normalized": [] } ]

[ { "id": "6262305_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked with an acetyl group" ], "offsets": [ [ 334, 362 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6262305_T3" }, { "role": "Site", "ref_id": "6262305_T5" } ] } ]

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[ { "id": "3286256__text", "type": "abstract", "text": [ "Primary structure of glycolate oxidase from spinach. \nThe primary structure of glycolate oxidase from spinach has been determined. Six different types of peptide digest were investigated, utilizing CNBr, proteolytic enzymes, and chemical modifications to change a specificity of cleavage. In total, 90 peptides were purified and analyzed. The studies were aimed at correlation with crystallographic analysis of the same protein carried through in parallel and with cDNA studies which utilized initially determined amino acid sequences for synthesis of oligonucleotide probes. Continuous comparisons with the results from the crystallographic studies helped at an early stage to secure peptide overlaps, at the same time as the peptide data secured residue assignments in the electron density maps. In the end, all data agree and regions from all parts of the molecule have been checked by independent methods of analysis. The primary structure establishes the type of N-terminal post-translational processing, and yields information on segments not fully defined in electron density maps. Combined, the chemical, crystallographic, and cDNA data give extensive reliability. The peptide analysis shows that the N-terminus is blocked by acylation of the initiator methionine, which is in a primary structure typical for non-removal of the methionine in the processing events of the nascent protein chain. The molecule is comparatively rich in menthionine and some other generally less common residues, but has only one cysteine residue and no extensive hydrophobic segment. An amino acid sequence homology with flavocytochrome b2 from yeast, as expected from known similarities in tertiary structure, is observed (33% residue identities). " ], "offsets": [ [ 0, 1736 ] ] } ]

[ { "id": "3286256_T1", "type": "Protein", "text": [ "glycolate oxidase" ], "offsets": [ [ 21, 38 ] ], "normalized": [] }, { "id": "3286256_T2", "type": "Protein", "text": [ "glycolate oxidase" ], "offsets": [ [ 79, 96 ] ], "normalized": [] }, { "id": "3286256_T3", "type": "Protein", "text": [ "flavocytochrome b2" ], "offsets": [ [ 1608, 1626 ] ], "normalized": [] }, { "id": "3286256_T5", "type": "Entity", "text": [ "initiator methionine" ], "offsets": [ [ 1251, 1271 ] ], "normalized": [] } ]

[ { "id": "3286256_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked by acylation" ], "offsets": [ [ 1223, 1243 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3286256_T2" }, { "role": "Site", "ref_id": "3286256_T5" } ] } ]

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[ { "id": "1191677__text", "type": "abstract", "text": [ "Human pituitary lutropin. Isolation, properties, and the complete amino acid sequence of the beta-subunit. \nThe separation of alpha and beta subunits from human pituitary lutropin is described, and the complete amino acid sequence of the beta subunit is proposed. It consists of 115 amino acids with serine and glycine at the amino and carboxyl termini, respectively. The single carbohydrate moiety is linked to asparagine in position 30 and the single tryptophan of the lutropin molecule is located at position 8. The two methionine residues in lutropin-beta are in positions 41 and 42. In addition to COOH-terminal heterogeneity, evidence for internal peptide cleavages was observed. " ], "offsets": [ [ 0, 686 ] ] } ]

[ { "id": "1191677_T1", "type": "Protein", "text": [ "beta-subunit" ], "offsets": [ [ 93, 105 ] ], "normalized": [] }, { "id": "1191677_T2", "type": "Protein", "text": [ "alpha" ], "offsets": [ [ 126, 131 ] ], "normalized": [] }, { "id": "1191677_T3", "type": "Protein", "text": [ "beta subunits" ], "offsets": [ [ 136, 149 ] ], "normalized": [] }, { "id": "1191677_T4", "type": "Protein", "text": [ "beta subunit" ], "offsets": [ [ 238, 250 ] ], "normalized": [] }, { "id": "1191677_T5", "type": "Protein", "text": [ "lutropin-beta" ], "offsets": [ [ 546, 559 ] ], "normalized": [] }, { "id": "1191677_T7", "type": "Entity", "text": [ "asparagine" ], "offsets": [ [ 412, 422 ] ], "normalized": [] }, { "id": "1191677_T8", "type": "Entity", "text": [ "tryptophan" ], "offsets": [ [ 453, 463 ] ], "normalized": [] } ]

[ { "id": "1191677_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate moiety is linked" ], "offsets": [ [ 379, 408 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1191677_T4" }, { "role": "Site", "ref_id": "1191677_T7" } ] }, { "id": "1191677_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate moiety is linked" ], "offsets": [ [ 379, 408 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1191677_T4" }, { "role": "Site", "ref_id": "1191677_T8" } ] } ]

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[ { "id": "2592374__text", "type": "abstract", "text": [ "Protein and carbohydrate structural analysis of a recombinant soluble CD4 receptor by mass spectrometry. \nThe primary structure of a soluble form of the CD4 receptor (sCD4) expressed in Chinese hamster ovary cells has been confirmed by mass spectrometric peptide mapping and and tandem mass spectrometry. These studies corroborated 95% of the 369-amino acid-long sequence and established the fidelity of translation of the NH2 and COOH terminal including the absence of \"ragged ends.\" The arrangement of the three disulfide bonds in recombinant sCD4 was also established by mass spectrometry and comparative high performance liquid chromatography mapping and shown to be identical to that expected from previous studies of intrachain disulfide bonding in T4 antigens derived from sheep and mouse. No other arrangements of disulfides were detected. Carbohydrate mapping by mass spectrometry was used to establish that both potential Asn-linked glycosylation sites in sCD4 (Asn271 and Asn300) have oligosaccharides attached. Structural characterization by mass spectrometry and methylation analysis of the heterogeneous family of oligosaccharides at each of the specific attachment sites indicates that the major components of both families of oligosaccharides have the following biantennary structures: (Formula, see text) where m + n = 0-2, and x = 0,1. Minor carbohydrate components having three N-acetylneuraminic acid (NeuAc) groups and an additional hexose-hexosamine unit were detected by high performance anion-exchange chromatography. " ], "offsets": [ [ 0, 1542 ] ] } ]

[ { "id": "2592374_T1", "type": "Protein", "text": [ "CD4 receptor" ], "offsets": [ [ 70, 82 ] ], "normalized": [] }, { "id": "2592374_T2", "type": "Protein", "text": [ "CD4 receptor" ], "offsets": [ [ 153, 165 ] ], "normalized": [] }, { "id": "2592374_T3", "type": "Protein", "text": [ "sCD4" ], "offsets": [ [ 167, 171 ] ], "normalized": [] }, { "id": "2592374_T4", "type": "Protein", "text": [ "sCD4" ], "offsets": [ [ 545, 549 ] ], "normalized": [] }, { "id": "2592374_T5", "type": "Protein", "text": [ "sCD4" ], "offsets": [ [ 966, 970 ] ], "normalized": [] }, { "id": "2592374_T6", "type": "Entity", "text": [ "Asn271" ], "offsets": [ [ 972, 978 ] ], "normalized": [] }, { "id": "2592374_T7", "type": "Entity", "text": [ "Asn300" ], "offsets": [ [ 983, 989 ] ], "normalized": [] } ]

[ { "id": "2592374_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "oligosaccharides attached" ], "offsets": [ [ 996, 1021 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2592374_T5" }, { "role": "Site", "ref_id": "2592374_T6" } ] }, { "id": "2592374_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "oligosaccharides attached" ], "offsets": [ [ 996, 1021 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2592374_T5" }, { "role": "Site", "ref_id": "2592374_T7" } ] } ]

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[ { "id": "9500918__text", "type": "abstract", "text": [ "Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus. \nWe used isothermal titration calorimetry and fluorescence spectroscopy to investigate the thermodynamics of non-sequence-specific DNA-binding by the Sso7d protein from the archaeon Sulfolobus solfataricus. We report the Sso7d-poly(dGdC) binding thermodynamics as a function of buffer composition (Tris-HCl or phosphate), temperature (15 to 45 degrees C), pH (7.1 to 8.0), osmotic stress and solvent (H2O/2H2O), and compare it to poly (dAdT) binding; and we have previously also reported the salt concentration dependence. Binding isotherms can be represented by the McGhee-von Hippel model for non-cooperative binding, with a binding site size of four to five DNA base-pairs and binding free energies in the range DeltaG degrees approximately -7 to DeltaG degrees approximately -10 kcal mol-1, depending on experimental conditions. The non-specific nature of the binding is reflected in similar thermodynamics for binding to poly(dAdT) and poly(dGdC). The native lysine methylation of Sso7d has only minor effects on the binding thermodynamics. Sso7d binding to poly(dGdC) is endothermic at 25 degrees C with a binding enthalpy DeltaH degrees approximately 10 kcal mol-1 in both phosphate and Tris-HCl buffers at pH 7.6, indicating that DeltaH degrees does not include large contributions from coupled buffer ionization equilibria at this pH. The binding enthalpy is temperature dependent with a measured heat capacity change DeltaCp degrees=-0.25(+/-0.01) kcal mol-1 K-1 and extrapolations of thermodynamic data indicate that the complex is heat stable with exothermic binding close to the growth temperature (75 to 80 degreesC) of S. solfataricus. Addition of neutral solutes (osmotic stress) has minor effects on DeltaG degrees and the exchange of H2O for 2H2O has only a small effect on DeltaH degrees, consistent with the inference that complex formation is not accompanied by net changes in surface hydration. Thus, other mechanisms for the heat capacity change must be found. The observed thermodynamics is discussed in relation to the nature of non-sequence-specific DNA-binding by proteins. " ], "offsets": [ [ 0, 2220 ] ] } ]

[ { "id": "9500918_T1", "type": "Protein", "text": [ "Sso7d" ], "offsets": [ [ 75, 80 ] ], "normalized": [] }, { "id": "9500918_T2", "type": "Protein", "text": [ "Sso7d" ], "offsets": [ [ 269, 274 ] ], "normalized": [] }, { "id": "9500918_T3", "type": "Protein", "text": [ "Sso7d" ], "offsets": [ [ 340, 345 ] ], "normalized": [] }, { "id": "9500918_T4", "type": "Protein", "text": [ "Sso7d" ], "offsets": [ [ 1105, 1110 ] ], "normalized": [] }, { "id": "9500918_T5", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 1083, 1089 ] ], "normalized": [] } ]

[ { "id": "9500918_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1090, 1101 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "9500918_T4" }, { "role": "Site", "ref_id": "9500918_T5" } ] } ]

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[ { "id": "8645219__text", "type": "abstract", "text": [ "Isolation of the murine S100 protein MRP14 (14 kDa migration-inhibitory-factor-related protein) from activated spleen cells: characterization of post-translational modifications and zinc binding. \nMRP14 (macrophage migration-inhibitory factor-related protein of molecular mass 14 kDa) is an S100 calcium binding protein constitutively expressed in human neutrophils which may be associated with cellular activation/inflammation. Murine MRP14 expression was up-regulated following concanavalin A activation of spleen cells, and the protein was isolated from conditioned medium in high yield (approx. 500 ng/ml). MRP14 had a mass of 12972 +/- 2 Da by electrospray ionization MS, whereas the theoretical mass derived from the cDNA sequence, after removal of the initiator Met, was 12918 Da, suggesting that the protein was post-translationally modified. We identified four post-translational modifications of MRP14: removal of the N-terminal Met, N-terminal acetylation, disulphide bond formation between Cys79 and Cys90, and 1-methylation of His106; the calculated mass was then 12971.8 Da. Methylation of His106 was further characterized after incubation of spleen cells with L-[methyl-3H]Met during concanavalin A stimulation. Sequential analysis of a peptide (obtained by digestion with Lys C) containing methylated His indicated that > 80% of the label in the cycle corresponded to His106, suggesting that the methyl residue was transferred from S-adenosyl-L-methionine. Comparison of the C18 reverse-phase HPLC retention times of phenylthiocarbamoyl derivatives of a hydrolysed digest peptide of MRP14 with those of standards confirmed methyl substitution on the 1-position of the imidazole ring. MRP14 bound more 85Zn2+ than the same amounts of the 10 kDa chemotactic protein (CP10) or S100 beta. Ca2+ decreased Zn2+ binding in S100 beta but it did not influence binding to MRP14, suggesting that the Zn2+ binding site was distinct from and independent of the two Ca2+ binding domains. " ], "offsets": [ [ 0, 1991 ] ] } ]

[ { "id": "8645219_T1", "type": "Protein", "text": [ "MRP14" ], "offsets": [ [ 37, 42 ] ], "normalized": [] }, { "id": "8645219_T2", "type": "Protein", "text": [ "MRP14" ], "offsets": [ [ 197, 202 ] ], "normalized": [] }, { "id": "8645219_T3", "type": "Protein", "text": [ "MRP14" ], "offsets": [ [ 436, 441 ] ], "normalized": [] }, { "id": "8645219_T4", "type": "Protein", "text": [ "concanavalin A" ], "offsets": [ [ 480, 494 ] ], "normalized": [] }, { "id": "8645219_T5", "type": "Protein", "text": [ "MRP14" ], "offsets": [ [ 611, 616 ] ], "normalized": [] }, { "id": "8645219_T6", "type": "Protein", "text": [ "MRP14" ], "offsets": [ [ 906, 911 ] ], "normalized": [] }, { "id": "8645219_T7", "type": "Protein", "text": [ "concanavalin A" ], "offsets": [ [ 1199, 1213 ] ], "normalized": [] }, { "id": "8645219_T8", "type": "Protein", "text": [ "MRP14" ], "offsets": [ [ 1599, 1604 ] ], "normalized": [] }, { "id": "8645219_T9", "type": "Protein", "text": [ "MRP14" ], "offsets": [ [ 1701, 1706 ] ], "normalized": [] }, { "id": "8645219_T10", "type": "Protein", "text": [ "CP10" ], "offsets": [ [ 1782, 1786 ] ], "normalized": [] }, { "id": "8645219_T11", "type": "Protein", "text": [ "MRP14" ], "offsets": [ [ 1879, 1884 ] ], "normalized": [] }, { "id": "8645219_T12", "type": "Entity", "text": [ "N-terminal" ], "offsets": [ [ 944, 954 ] ], "normalized": [] }, { "id": "8645219_T15", "type": "Entity", "text": [ "His106" ], "offsets": [ [ 1040, 1046 ] ], "normalized": [] }, { "id": "8645219_T17", "type": "Entity", "text": [ "His106" ], "offsets": [ [ 1104, 1110 ] ], "normalized": [] }, { "id": "8645219_T19", "type": "Entity", "text": [ "His" ], "offsets": [ [ 1317, 1320 ] ], "normalized": [] } ]

[ { "id": "8645219_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 955, 966 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8645219_T6" }, { "role": "Site", "ref_id": "8645219_T12" } ] }, { "id": "8645219_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "1-methylation" ], "offsets": [ [ 1023, 1036 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8645219_T6" }, { "role": "Site", "ref_id": "8645219_T15" } ] }, { "id": "8645219_E3", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "Methylation" ], "offsets": [ [ 1089, 1100 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8645219_T6" }, { "role": "Site", "ref_id": "8645219_T17" } ] }, { "id": "8645219_E4", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 1306, 1316 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8645219_T6" }, { "role": "Site", "ref_id": "8645219_T19" } ] } ]

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[ { "id": "8344916__text", "type": "abstract", "text": [ "Amino acid exchange and covalent modification by cysteine and glutathione explain isoforms of fatty acid-binding protein occurring in bovine liver. \nA unique property of the liver-type member of the family of fatty acid-binding proteins is the heterogeneic pattern observed upon isolation, which can only partly be ascribed to the state of lipidation. Here we unraveled the structural basis of the heterogeneity of delipidated liver-type fatty acid-binding protein (L-FABP). Charge fractions of L-FABP focusing at pH 6.0 and at pH 7.0/7.1 were first isolated from bovine liver. Upon reduction, however, two distinct isoforms, namely pI 6.0 L-FABP and pI 7.0 L-FABP, were observed. From these isoforms peptides were generated enzymically and chemically by four independent methods. Peptides were separated by reverse phase high performance liquid chromatography and analyzed by Edman degradation and plasma desorption mass spectrometry. The complete amino acid sequences of the isoforms were established; they consist of 127 amino acids and each is N-terminally blocked with an acetyl group. The difference between pI 6.0 L-FABP and pI 7.0 L-FABP was attributed to an asparagine-aspartate exchange at position 105. When tryptic peptides of the pH 7.0/7.1 fraction were analyzed, discrepancies between sequence and mass data of the peptides containing at position 69 the sole cysteine of L-FABP led to the disclosure of a cysteinylation occurring at this position and giving rise to the slightly more basic pH 7.1 species. Moreover, chemical modification studies revealed that a part of the pH 6.0 fraction was pI 7.0 L-FABP that was glutathionylated at Cys69. Neither modification, however, prevented the binding of fatty acids. Together amino acid exchange and covalent modification of cysteine entirely explain the heterogeneity of L-FABP from bovine liver. " ], "offsets": [ [ 0, 1859 ] ] } ]

[ { "id": "8344916_T1", "type": "Protein", "text": [ "liver-type fatty acid-binding protein" ], "offsets": [ [ 427, 464 ] ], "normalized": [] }, { "id": "8344916_T2", "type": "Protein", "text": [ "L-FABP" ], "offsets": [ [ 466, 472 ] ], "normalized": [] }, { "id": "8344916_T3", "type": "Protein", "text": [ "L-FABP" ], "offsets": [ [ 495, 501 ] ], "normalized": [] }, { "id": "8344916_T4", "type": "Protein", "text": [ "L-FABP" ], "offsets": [ [ 658, 664 ] ], "normalized": [] }, { "id": "8344916_T5", "type": "Protein", "text": [ "L-FABP" ], "offsets": [ [ 1121, 1127 ] ], "normalized": [] }, { "id": "8344916_T6", "type": "Protein", "text": [ "L-FABP" ], "offsets": [ [ 1139, 1145 ] ], "normalized": [] }, { "id": "8344916_T7", "type": "Protein", "text": [ "L-FABP" ], "offsets": [ [ 1386, 1392 ] ], "normalized": [] }, { "id": "8344916_T8", "type": "Protein", "text": [ "L-FABP" ], "offsets": [ [ 1616, 1622 ] ], "normalized": [] }, { "id": "8344916_T9", "type": "Protein", "text": [ "L-FABP" ], "offsets": [ [ 1833, 1839 ] ], "normalized": [] }, { "id": "8344916_T10", "type": "Entity", "text": [ "N-terminally" ], "offsets": [ [ 1048, 1060 ] ], "normalized": [] } ]

[ { "id": "8344916_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "N-terminally blocked with an acetyl group" ], "offsets": [ [ 1048, 1089 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8344916_T4" }, { "role": "Site", "ref_id": "8344916_T10" } ] } ]

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[ { "id": "6264908__text", "type": "abstract", "text": [ "Amino acid sequence studies on sheep liver fructose-bisphosphatase. I. The S-peptide. \nFructose-bisphosphatase has been isolated from sheep liver using affinity-elution chromatography from carboxymethylcellulose as the final purification step. The purified enzyme was homogeneous by disc gel electrophoresis. Digestion with subtilisin yielded the N-terminal S-peptide similar to that reported for the rabbit and pig. The peptide has an acetylated amino terminal residue and the following sequence deduced from a study of the tryptic and cyanogen bromide peptides: Ac-Thr-Asp-Glu-Ala-Pro-Phe-Asp-Thr-Asn-Ile-Val-Thr-Val-Thr-Arg-Phe-Val-Met-Glu-Glu-Gly-Arg-Lys-Ala-Arg-Gly-Thr-Gly-Glu-Met-Thr-Gln-Leu-Leu-Asn-Ser-Leu-Cys-Thr-Ala-Val-Lys-Ala-Ile-Ser-Thr-Ala-Val-Arg-Lys-Ala-Gly-Ile-Ala-His -Leu-Tyr-Gly-Ile-Ala. The sheep liver S-peptide sequence shows only six changes in 60 residues and three changes in 56 residues compared with the sequences of the rabbit and pig S-peptides respectively. " ], "offsets": [ [ 0, 990 ] ] } ]

[ { "id": "6264908_T1", "type": "Protein", "text": [ "fructose-bisphosphatase. I" ], "offsets": [ [ 43, 69 ] ], "normalized": [] }, { "id": "6264908_T2", "type": "Protein", "text": [ "Fructose-bisphosphatase" ], "offsets": [ [ 87, 110 ] ], "normalized": [] }, { "id": "6264908_T4", "type": "Entity", "text": [ "amino terminal residue" ], "offsets": [ [ 447, 469 ] ], "normalized": [] } ]

[ { "id": "6264908_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 436, 446 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6264908_T2" }, { "role": "Site", "ref_id": "6264908_T4" } ] } ]

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[ { "id": "7338518__text", "type": "abstract", "text": [ "Amino acid sequence of calmodulin from scallop (Patinopecten) adductor muscle. \nThe complete amino acid sequence of scallop calmodulin was determined by isolating and sequencing the peptides obtained after cyanogen bromide cleavage and tryptic digestion. The protein consisted of 148 amino acid residues and its amino(N)-terminus was blocked with an acetyl group. Scallop calmodulin lacked tryptophan and cysteine residues and contained one mol each of N epsilon-trimethyllysine (Tml) and histidine residues per mol of the protein. Scallop calmodulin contained only one tyrosine residue, while vertebrate calmodulins contain two. On comparing its amino acid sequence with that of bovine calmodulin, three amino acid substitutions were found at positions 99(Tyr leads to Phe), 143(Gln leads to Thr), and 147(Ala leads to Ser). " ], "offsets": [ [ 0, 826 ] ] } ]

[ { "id": "7338518_T1", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 23, 33 ] ], "normalized": [] }, { "id": "7338518_T2", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 124, 134 ] ], "normalized": [] }, { "id": "7338518_T3", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 372, 382 ] ], "normalized": [] }, { "id": "7338518_T4", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 540, 550 ] ], "normalized": [] }, { "id": "7338518_T5", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 687, 697 ] ], "normalized": [] }, { "id": "7338518_T6", "type": "Entity", "text": [ "amino(N)-terminus" ], "offsets": [ [ 312, 329 ] ], "normalized": [] } ]

[ { "id": "7338518_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked with an acetyl group" ], "offsets": [ [ 334, 362 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7338518_T2" }, { "role": "Site", "ref_id": "7338518_T6" } ] } ]

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[ { "id": "8243648__text", "type": "abstract", "text": [ "Determination and mutational analysis of the phosphorylation site in the hypusine-containing protein Hyp2p. \nElectrospray mass spectrometry of the purified isoforms of the hypusine-containing protein of Saccharomyces cerevisiae Hyp2p suggested a phosphorylation of the acidic isoform, which was confirmed by phosphatase treatment. The phosphorylation site was mapped to the N-acetylated serine residue in position no. 1 by mass spectrometric analysis of enzymatic fragments. Mutation of this serine residue gives rise to only the basic isoform, confirming our protein chemical data. As this mutation has no effect on cell viability or growth rate, the unphosphorylated isoform is sufficient to exert the essential in vivo function of Hyp2p. " ], "offsets": [ [ 0, 741 ] ] } ]

[ { "id": "8243648_T1", "type": "Protein", "text": [ "hypusine-containing protein" ], "offsets": [ [ 73, 100 ] ], "normalized": [] }, { "id": "8243648_T2", "type": "Protein", "text": [ "Hyp2p" ], "offsets": [ [ 101, 106 ] ], "normalized": [] }, { "id": "8243648_T3", "type": "Protein", "text": [ "hypusine-containing protein" ], "offsets": [ [ 172, 199 ] ], "normalized": [] }, { "id": "8243648_T4", "type": "Protein", "text": [ "Hyp2p" ], "offsets": [ [ 228, 233 ] ], "normalized": [] }, { "id": "8243648_T5", "type": "Protein", "text": [ "Hyp2p" ], "offsets": [ [ 734, 739 ] ], "normalized": [] }, { "id": "8243648_T8", "type": "Entity", "text": [ "serine" ], "offsets": [ [ 387, 393 ] ], "normalized": [] } ]

[ { "id": "8243648_E1", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 246, 261 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8243648_T4" } ] }, { "id": "8243648_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "N-acetylated" ], "offsets": [ [ 374, 386 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8243648_T4" }, { "role": "Site", "ref_id": "8243648_T8" } ] } ]

[ { "id": "8243648_1", "entity_ids": [ "8243648_T1", "8243648_T2" ] } ]

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[ { "id": "2190986__text", "type": "abstract", "text": [ "Purification and characterization of rho-crystallin from Japanese common bullfrog lens. \nIn a previous paper, we reported that the partial amino acid sequence (225 residues) from the COOH terminus of rho-crystallin from European common frog lens shows 77% similarity to that of prostaglandin (PG) F synthetase, an aldo-keto reductase, from bovine lung (Watanabe, K., Fujii, Y., Nakayama, K., Ohkubo, H., Kuramitsu, S., Kagamiyama, H., Nakanishi, S., and Hayaishi, O. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 11-15). Here rho-crystallin was purified to apparent homogeneity from the eye lens of the Japanese common bullfrog (Rana catesbeiana) by four sequential chromatographies using Sephadex G-100, Red Sepharose, and dual Mono S. Two types of rho-crystallin, RHO-I and RHO-II, named according to their elution order from a Mono S column, are essentially identical in terms of immunochemical properties, amino acid composition, and partial amino acid sequence. But the NH2-terminal Thr of RHO-I is blocked with an acyl group, while that of RHO-II is free. Both crystallins as well as PGF synthetase are monomeric proteins with a molecular weight of about 35,000 and they have the ability to bind NADPH with a stoichiometry of 0.75 mol of cofactor/mol of protein. Although rho-crystallin does not cross-react with antibody against PGF synthetase, the NH2-terminal amino acid sequence (107 residues) of rho-crystallin shows 77% similarity to that of the enzyme. However, PGD2, PGE2, 9,10-phenanthrenequinone, p-nitrobenzaldehyde, DL-glyceraldehyde, D-glucuronic acid, D-glucose, D-xylose, menadione, p-nitroacetophenone, dihydroxyacetone, succinic semialdehyde, phenylglyoxal, and testosterone were not substrates for these crystallins. PGH2 9,11-endoperoxide reductase activities of RHO-I and RHO-II were 1.3 and 1.0 milliunits/mg of protein, respectively, which are only about 2% of that of bovine lung PGF synthetase. These results indicate that the rho-crystallins RHO-I and RHO-II belong to a group of aldo-keto reductases based on primary structure, molecular properties, and NADPH-binding ability, but show only low PGH2 9,11-endoperoxide reductase activity. " ], "offsets": [ [ 0, 2165 ] ] } ]

[ { "id": "2190986_T1", "type": "Protein", "text": [ "RHO-I" ], "offsets": [ [ 761, 766 ] ], "normalized": [] }, { "id": "2190986_T2", "type": "Protein", "text": [ "RHO-II" ], "offsets": [ [ 771, 777 ] ], "normalized": [] }, { "id": "2190986_T3", "type": "Protein", "text": [ "RHO-I" ], "offsets": [ [ 990, 995 ] ], "normalized": [] }, { "id": "2190986_T4", "type": "Protein", "text": [ "RHO-I" ], "offsets": [ [ 1041, 1046 ] ], "normalized": [] }, { "id": "2190986_T5", "type": "Protein", "text": [ "RHO-I" ], "offsets": [ [ 1783, 1788 ] ], "normalized": [] }, { "id": "2190986_T6", "type": "Protein", "text": [ "RHO-II" ], "offsets": [ [ 1793, 1799 ] ], "normalized": [] }, { "id": "2190986_T7", "type": "Protein", "text": [ "RHO-I" ], "offsets": [ [ 1968, 1973 ] ], "normalized": [] }, { "id": "2190986_T8", "type": "Protein", "text": [ "RHO-II" ], "offsets": [ [ 1978, 1984 ] ], "normalized": [] }, { "id": "2190986_T9", "type": "Entity", "text": [ "Thr" ], "offsets": [ [ 983, 986 ] ], "normalized": [] } ]

[ { "id": "2190986_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked with an acyl group" ], "offsets": [ [ 999, 1025 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2190986_T3" }, { "role": "Site", "ref_id": "2190986_T9" } ] }, { "id": "2190986_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "free" ], "offsets": [ [ 1051, 1055 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2190986_T4" }, { "role": "Site", "ref_id": "2190986_T9" } ] } ]

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[ { "id": "6266492__text", "type": "abstract", "text": [ "Collagen biosynthesis by human skin fibroblasts. III. The effects of ascorbic acid on procollagen production and prolyl hydroxylase activity. \nHuman skin fibroblasts were cultured under conditions optimized for collagen synthesis, and the effects of ascorbic acid on procollagen production, proline hydroxylation and the activity of prolyl hydroxylase were examined in cultures. the results indicated that addition of ascorbic acid to confluent monolayer cultures of adult human skin fibroblasts markedly increased the amount of [3H]hydroxyproline synthesized. Ascorbic acid, however, did not increase the synthesis of 3H-labeled collagenous polypeptides assayed independently of hydroxylation of proline residues, nor did it affect the amount of prolyl hydroxylase detectable by an in vitro enzyme assay. Also long-term cultures of the cells or initiation of fibroblast cultures in the presence of ascorbic acid did not lead to an apparent selection of a cell population which might be abnormally responsive to ascorbic acid. Thus, ascorbic acid appears to have one primary action on the synthesis of procollagen by cultured human skin fibroblasts: it is necessary for synthesis of hydroxyproline, and consequently for proper triple helix formation and secretion of procollagen. " ], "offsets": [ [ 0, 1280 ] ] } ]

[ { "id": "6266492_T1", "type": "Protein", "text": [ "Collagen" ], "offsets": [ [ 0, 8 ] ], "normalized": [] }, { "id": "6266492_T2", "type": "Protein", "text": [ "procollagen" ], "offsets": [ [ 267, 278 ] ], "normalized": [] }, { "id": "6266492_T3", "type": "Protein", "text": [ "procollagen" ], "offsets": [ [ 1267, 1278 ] ], "normalized": [] }, { "id": "6266492_T4", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 291, 298 ] ], "normalized": [] }, { "id": "6266492_T7", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 697, 704 ] ], "normalized": [] } ]

[ { "id": "6266492_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 299, 312 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6266492_T2" }, { "role": "Site", "ref_id": "6266492_T4" } ] }, { "id": "6266492_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 680, 693 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6266492_T2" }, { "role": "Site", "ref_id": "6266492_T7" } ] } ]

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[ { "id": "4447620__text", "type": "abstract", "text": [ "Age-related variations in hydroxylation of lysine and proline in collagen. \nThe effect of age on the extent of hydroxylation of lysine and proline both generally and at certain specific sites in collagens from bone, skin and tendon was examined in the chick from the 14-day embryo to the 18-month-old adult. For all collagens there was a marked fall in the overall extent of hydroxylation of lysine with increasing age in both alpha(1) and alpha(2) chains, this fall occurring mostly in a relatively short period immediately after hatching. Hydroxylation of lysine declined to a constant value which, as expected, differed appreciably for each collagen and was considered to be characteristic of the collagen according to its tissue of origin. Hydroxylation of lysine in the N-terminal, non-helical telopeptide region of both alpha(1) and alpha(2) chains, which is important with regard to cross-linking, was relatively high in embryonic collagens. There was, however, a rapid loss of hydroxylation at these sites in skin collagen, occurring both during development of the embryo and in the period immediately after hatching. In contrast some hydroxylation at these sites persisted in bone and tendon collagens and, as judged by examination of peptide alpha(1)-CB1, appeared to reach a constant value in time of about 33% in bone and about 15% in tendon collagen. The actual extent of hydroxylation of lysine in the N-terminal telopeptides and the size of the changes in these values with age appeared to be unrelated to the corresponding whole-chain values, and it is suggested therefore that hydroxylation of telopeptidyl lysine may be under separate enzymic control. The increased hydroxylation of lysine in the embryo was accompanied by only minimal changes in proline hydroxylation, which was very slightly increased in embryonic bone and tendon collagens. Increased hydroxylation of proline in the embryo was, however, readily observed in peptide alpha(1)-CB2 from the helical region of tendon collagen. This hydroxylation was close to the theoretical maximum, in contrast with that observed in post-embryonic tendon, where hydroxylation was incomplete, as in rat tendon (Bornstein, 1967), only four on average, of the six susceptible proline residues being hydroxylated. " ], "offsets": [ [ 0, 2278 ] ] } ]

[ { "id": "4447620_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 65, 73 ] ], "normalized": [] }, { "id": "4447620_T2", "type": "Protein", "text": [ "collagens" ], "offsets": [ [ 195, 204 ] ], "normalized": [] }, { "id": "4447620_T3", "type": "Protein", "text": [ "collagens" ], "offsets": [ [ 316, 325 ] ], "normalized": [] }, { "id": "4447620_T4", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 644, 652 ] ], "normalized": [] }, { "id": "4447620_T5", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 700, 708 ] ], "normalized": [] }, { "id": "4447620_T6", "type": "Protein", "text": [ "collagens" ], "offsets": [ [ 938, 947 ] ], "normalized": [] }, { "id": "4447620_T7", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 1022, 1030 ] ], "normalized": [] }, { "id": "4447620_T8", "type": "Protein", "text": [ "collagens" ], "offsets": [ [ 1201, 1210 ] ], "normalized": [] }, { "id": "4447620_T9", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 1354, 1362 ] ], "normalized": [] }, { "id": "4447620_T10", "type": "Protein", "text": [ "collagens" ], "offsets": [ [ 1851, 1860 ] ], "normalized": [] }, { "id": "4447620_T11", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 2000, 2008 ] ], "normalized": [] }, { "id": "4447620_T13", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 43, 49 ] ], "normalized": [] }, { "id": "4447620_T14", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 54, 61 ] ], "normalized": [] }, { "id": "4447620_T16", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 128, 134 ] ], "normalized": [] }, { "id": "4447620_T17", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 139, 146 ] ], "normalized": [] }, { "id": "4447620_T19", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 392, 398 ] ], "normalized": [] }, { "id": "4447620_T21", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 558, 564 ] ], "normalized": [] }, { "id": "4447620_T23", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 761, 767 ] ], "normalized": [] }, { "id": "4447620_T24", "type": "Entity", "text": [ "non-helical telopeptide region" ], "offsets": [ [ 787, 817 ] ], "normalized": [] }, { "id": "4447620_T28", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 1402, 1408 ] ], "normalized": [] }, { "id": "4447620_T30", "type": "Entity", "text": [ "telopeptidyl lysine" ], "offsets": [ [ 1611, 1630 ] ], "normalized": [] }, { "id": "4447620_T32", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 1701, 1707 ] ], "normalized": [] }, { "id": "4447620_T34", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 1889, 1896 ] ], "normalized": [] }, { "id": "4447620_T35", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 2241, 2248 ] ], "normalized": [] } ]

[ { "id": "4447620_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 26, 39 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T1" }, { "role": "Site", "ref_id": "4447620_T13" } ] }, { "id": "4447620_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 26, 39 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T1" }, { "role": "Site", "ref_id": "4447620_T14" } ] }, { "id": "4447620_E3", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 111, 124 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T2" }, { "role": "Site", "ref_id": "4447620_T16" } ] }, { "id": "4447620_E4", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 111, 124 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T2" }, { "role": "Site", "ref_id": "4447620_T17" } ] }, { "id": "4447620_E5", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 375, 388 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T3" }, { "role": "Site", "ref_id": "4447620_T19" } ] }, { "id": "4447620_E6", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "Hydroxylation" ], "offsets": [ [ 541, 554 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T4" }, { "role": "Site", "ref_id": "4447620_T21" } ] }, { "id": "4447620_E7", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "Hydroxylation" ], "offsets": [ [ 744, 757 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T6" }, { "role": "Site", "ref_id": "4447620_T23" } ] }, { "id": "4447620_E8", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 985, 998 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T7" }, { "role": "Site", "ref_id": "4447620_T24" } ] }, { "id": "4447620_E9", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1143, 1156 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T8" }, { "role": "Site", "ref_id": "4447620_T24" } ] }, { "id": "4447620_E10", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1385, 1398 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T9" }, { "role": "Site", "ref_id": "4447620_T28" } ] }, { "id": "4447620_E11", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1594, 1607 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T9" }, { "role": "Site", "ref_id": "4447620_T30" } ] }, { "id": "4447620_E12", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1684, 1697 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T10" }, { "role": "Site", "ref_id": "4447620_T32" } ] }, { "id": "4447620_E13", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1872, 1885 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T11" }, { "role": "Site", "ref_id": "4447620_T34" } ] }, { "id": "4447620_E14", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 2264, 2276 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4447620_T11" }, { "role": "Site", "ref_id": "4447620_T35" } ] } ]

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[ { "id": "320204__text", "type": "abstract", "text": [ "Primary structure of rabbit skeletal muscle troponin-T. Sequence determination of the NH2-terminal fragment CB3 and the complete sequence of troponin-T. \nThe amino acid sequence of CB3, the NH2-terminal fragment of troponin-T, and the alignment of all six cyanogen bromide (CB) fragments are reported. Fragment CB3, comprised of 70 residues, has eight of the nine prolines of troponin-T. As observed in other proteins of the myofibrillar system, its NH2 terminus is blocked by an acetyl group. Methionine-containing \"overlap\" peptides isolated from a peptic digest of troponin-T as well as 2-(2-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine cleavage of the protein were used to order the fragments as CB3-CB2-CB5-CB4-CB7-CB6. The complete sequence of troponin-T, a single polypeptide chain of 259 amino acids having a molecular weight of 30,500, is presented. " ], "offsets": [ [ 0, 863 ] ] } ]

[ { "id": "320204_T1", "type": "Protein", "text": [ "troponin-T" ], "offsets": [ [ 44, 54 ] ], "normalized": [] }, { "id": "320204_T2", "type": "Protein", "text": [ "troponin-T" ], "offsets": [ [ 141, 151 ] ], "normalized": [] }, { "id": "320204_T3", "type": "Protein", "text": [ "troponin-T" ], "offsets": [ [ 215, 225 ] ], "normalized": [] }, { "id": "320204_T4", "type": "Protein", "text": [ "troponin-T" ], "offsets": [ [ 376, 386 ] ], "normalized": [] }, { "id": "320204_T5", "type": "Protein", "text": [ "troponin-T" ], "offsets": [ [ 568, 578 ] ], "normalized": [] }, { "id": "320204_T6", "type": "Protein", "text": [ "troponin-T" ], "offsets": [ [ 754, 764 ] ], "normalized": [] }, { "id": "320204_T7", "type": "Entity", "text": [ "NH2 terminus" ], "offsets": [ [ 450, 462 ] ], "normalized": [] } ]

[ { "id": "320204_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked by an acetyl group" ], "offsets": [ [ 466, 492 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "320204_T4" }, { "role": "Site", "ref_id": "320204_T7" } ] } ]

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[ { "id": "6290217__text", "type": "abstract", "text": [ "Complete primary structure of protein phosphatase inhibitor-1 from rabbit skeletal muscle. \nThe complete primary structure of protein phosphatase inhibitor-1 has been determined. The protein consists of a single polypeptide chain of 165 residues, molecular weight 18640. The threonine residue that must be phosphorylated for activation is at position 35 and the active cyanogen bromide peptide, CB-1, comprises residues 2-66. The N-terminal methionine is acetylated and 40% of the inhibitor-1 molecules lack the C-terminal dipeptide Ala-Val. Serine-67 is substantially phosphorylated in vivo, but this phosphoserine residue does not appear to influence the activity of inhibitor-1. " ], "offsets": [ [ 0, 682 ] ] } ]

[ { "id": "6290217_T1", "type": "Protein", "text": [ "protein phosphatase inhibitor-1" ], "offsets": [ [ 30, 61 ] ], "normalized": [] }, { "id": "6290217_T2", "type": "Protein", "text": [ "protein phosphatase inhibitor-1" ], "offsets": [ [ 126, 157 ] ], "normalized": [] }, { "id": "6290217_T3", "type": "Protein", "text": [ "inhibitor-1" ], "offsets": [ [ 481, 492 ] ], "normalized": [] }, { "id": "6290217_T4", "type": "Protein", "text": [ "inhibitor-1" ], "offsets": [ [ 669, 680 ] ], "normalized": [] }, { "id": "6290217_T5", "type": "Entity", "text": [ "threonine" ], "offsets": [ [ 275, 284 ] ], "normalized": [] }, { "id": "6290217_T7", "type": "Entity", "text": [ "methionine" ], "offsets": [ [ 441, 451 ] ], "normalized": [] }, { "id": "6290217_T9", "type": "Entity", "text": [ "Serine-67" ], "offsets": [ [ 542, 551 ] ], "normalized": [] } ]

[ { "id": "6290217_E1", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 306, 320 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6290217_T2" }, { "role": "Site", "ref_id": "6290217_T5" } ] }, { "id": "6290217_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 455, 465 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6290217_T3" }, { "role": "Site", "ref_id": "6290217_T7" } ] }, { "id": "6290217_E3", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 569, 583 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6290217_T4" }, { "role": "Site", "ref_id": "6290217_T9" } ] } ]

[ { "id": "6290217_1", "entity_ids": [ "6290217_T3", "6290217_T3" ] }, { "id": "6290217_2", "entity_ids": [ "6290217_T4", "6290217_T4" ] } ]

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[ { "id": "4351077__text", "type": "abstract", "text": [ "Quantum chemical study of the mechanism of collagen proline hydroxylation. \n" ], "offsets": [ [ 0, 76 ] ] } ]

[ { "id": "4351077_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 43, 51 ] ], "normalized": [] }, { "id": "4351077_T2", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 52, 59 ] ], "normalized": [] } ]

[ { "id": "4351077_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 60, 73 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4351077_T1" }, { "role": "Site", "ref_id": "4351077_T2" } ] } ]

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[ { "id": "3905433__text", "type": "abstract", "text": [ "In vitro methylation of the elongation factor EF-Tu from Escherichia coli. \nThe in vitro methylation of the elongation factor EF-Tu from Escherichia coli was investigated. The methylation of newly synthesized EF-Tu was obtained using lambda rifd 18 DNA as template and S-adenosyl [methyl-3H]methionine as methyl donor. About 3 mol methyl residues were incorporated for every 10 mol EF-Tu synthesized. Analysis of the nature of the methyl-containing residues by protein hydrolysis followed by paper chromatography showed that both mono- and dimethyllysine were present. The methylation of EF-Tu was also studied separately from its synthesis by using cell-free systems with artificially undermethylated components. " ], "offsets": [ [ 0, 714 ] ] } ]

[ { "id": "3905433_T1", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 46, 51 ] ], "normalized": [] }, { "id": "3905433_T2", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 126, 131 ] ], "normalized": [] }, { "id": "3905433_T3", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 209, 214 ] ], "normalized": [] }, { "id": "3905433_T4", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 382, 387 ] ], "normalized": [] }, { "id": "3905433_T5", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 588, 593 ] ], "normalized": [] } ]

[ { "id": "3905433_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 9, 20 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3905433_T1" } ] }, { "id": "3905433_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 89, 100 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3905433_T2" } ] }, { "id": "3905433_E3", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 573, 584 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3905433_T5" } ] } ]

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[ { "id": "10422846__text", "type": "abstract", "text": [ "Determination of the complete covalent structure of the major glycoform of DQH sperm surface protein, a novel trypsin-resistant boar seminal plasma O-glycoprotein related to pB1 protein. \nThe complete covalent structure of a novel boar DQH sperm surface protein resistant to many classical procedures of enzymatic fragmentation was determined. The relative molecular mass of the major form of this protein determined by ESI-MS and MALDI-MS was 13,065.2+/-1.0 and 13,065.1, respectively. However, additional peaks differing by 162 Da (i.e., minus hexose), 365 Da (i.e., minus hexose and N-acetylhexosamine), 146 Da (i.e., plus deoxyhexose), and 291 Da (i.e., plus sialic acid) indicated the heterogeneity due to differences in glycosylation. The complete covalent structure of the protein was determined using automated Edman degradation, MALDI-MS, and post-source decay (PSD) MALDI-MS, and shown to consist of N-terminal O-glycosylated peptide followed by two fibronectin type II repeats. The carbohydrates are O-glycosidically linked to threonine 10, as confirmed by PSD MALDI-MS of the isolated N-terminal glycopeptide. Eight cysteine residues of the protein form four disulfide bridges, the positions of which were assigned from MALDI-MS and Edman degradation data. We conclude that mass spectral techniques provide an indispensable tool for the detailed analysis of the covalent structure of proteins, especially those that are refractory to standard approaches of protein chemistry. " ], "offsets": [ [ 0, 1488 ] ] } ]

[ { "id": "10422846_T1", "type": "Protein", "text": [ "DQH" ], "offsets": [ [ 75, 78 ] ], "normalized": [] }, { "id": "10422846_T2", "type": "Protein", "text": [ "pB1" ], "offsets": [ [ 174, 177 ] ], "normalized": [] }, { "id": "10422846_T3", "type": "Protein", "text": [ "DQH" ], "offsets": [ [ 236, 239 ] ], "normalized": [] }, { "id": "10422846_T5", "type": "Entity", "text": [ "threonine 10" ], "offsets": [ [ 1038, 1050 ] ], "normalized": [] } ]

[ { "id": "10422846_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrates are O-glycosidically linked" ], "offsets": [ [ 993, 1034 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "10422846_T3" }, { "role": "Site", "ref_id": "10422846_T5" } ] } ]

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[ { "id": "2361960__text", "type": "abstract", "text": [ "Structure of recombinant human interleukin 5 produced by Chinese hamster ovary cells. \nThe complete peptide map of purified recombinant human interleukin 5 (rhIL-5) was determined to verify its primary structure, glycosylation sites, and disulfide bonding structure. Each peptide fragment generated by Achromobacter protease I (API) digestion was purified and characterized by amino acid analysis and amino acid sequence analysis. After digestion with API, we could identify all the peptides which were expected from human IL-5 cDNA sequence. The analyses of sulfhydryl content in rhIL-5 molecule and disulfide-containing peptide obtained from API digestion indicated that active form of rhIL-5 existed as an antiparallel dimer linked by two pairs of Cys-44 and Cys-86. In addition, we concluded that Thr-3 and Asn-28 were glycosylated. The results indicate that primary structure of rhIL-5 is highly homogeneous and observed heterogeneity is due to the difference in the content of carbohydrate. " ], "offsets": [ [ 0, 1002 ] ] } ]

[ { "id": "2361960_T1", "type": "Protein", "text": [ "interleukin 5" ], "offsets": [ [ 142, 155 ] ], "normalized": [] }, { "id": "2361960_T2", "type": "Protein", "text": [ "IL-5" ], "offsets": [ [ 159, 163 ] ], "normalized": [] }, { "id": "2361960_T3", "type": "Protein", "text": [ "IL-5" ], "offsets": [ [ 525, 529 ] ], "normalized": [] }, { "id": "2361960_T4", "type": "Protein", "text": [ "IL-5" ], "offsets": [ [ 586, 590 ] ], "normalized": [] }, { "id": "2361960_T5", "type": "Protein", "text": [ "IL-5" ], "offsets": [ [ 693, 697 ] ], "normalized": [] }, { "id": "2361960_T6", "type": "Protein", "text": [ "IL-5" ], "offsets": [ [ 891, 895 ] ], "normalized": [] }, { "id": "2361960_T7", "type": "Entity", "text": [ "rhIL-5" ], "offsets": [ [ 157, 163 ] ], "normalized": [] }, { "id": "2361960_T8", "type": "Entity", "text": [ "rhIL-5 molecule" ], "offsets": [ [ 584, 599 ] ], "normalized": [] }, { "id": "2361960_T9", "type": "Entity", "text": [ "rhIL-5" ], "offsets": [ [ 691, 697 ] ], "normalized": [] }, { "id": "2361960_T10", "type": "Entity", "text": [ "Thr-3" ], "offsets": [ [ 805, 810 ] ], "normalized": [] }, { "id": "2361960_T11", "type": "Entity", "text": [ "Asn-28" ], "offsets": [ [ 815, 821 ] ], "normalized": [] }, { "id": "2361960_T13", "type": "Entity", "text": [ "rhIL-5" ], "offsets": [ [ 889, 895 ] ], "normalized": [] } ]

[ { "id": "2361960_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 827, 839 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2361960_T5" }, { "role": "Site", "ref_id": "2361960_T10" } ] }, { "id": "2361960_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 827, 839 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2361960_T5" }, { "role": "Site", "ref_id": "2361960_T11" } ] } ]

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[ { "id": "5165523__text", "type": "abstract", "text": [ "Chromatographic separation of the enzymes required for hydroxylation of lysine and proline residues of protocollagen. \n" ], "offsets": [ [ 0, 119 ] ] } ]

[ { "id": "5165523_T1", "type": "Protein", "text": [ "protocollagen" ], "offsets": [ [ 103, 116 ] ], "normalized": [] }, { "id": "5165523_T3", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 72, 78 ] ], "normalized": [] }, { "id": "5165523_T4", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 83, 90 ] ], "normalized": [] } ]

[ { "id": "5165523_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 55, 68 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "5165523_T1" }, { "role": "Site", "ref_id": "5165523_T3" } ] }, { "id": "5165523_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 55, 68 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "5165523_T1" }, { "role": "Site", "ref_id": "5165523_T4" } ] } ]

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[ { "id": "407930__text", "type": "abstract", "text": [ "Primary structure of human J chain: alignment of peptides from chemical and enzymatic hydrolyses. \nThe primary structure of the J chain from a human Waldenstroms IgM protein has been determined using a combination of automated and conventional Edman degradative procedures. Eighty-five percent of the sequence was established with peptides isolated from tryptic digests of carboxyamidomethylated and citraconylated J chain, many of which were sequenced completely. Alignment of the tryptic fragments was achieved with peptides generated by chymotrypsin and limited acid hydrolyses. The j chain consits of 129 amino acids and a single oligosaccharide structure linked to asparagine at positon 43 of the sequence. The molecular weight, including 7.5% carbohydrate by weight, is 16 422. The location and arrangement of three half-cystines could be deduced from previous studies, whereas the pairing of the remaining five disulfide bonds still needs to be clarified. " ], "offsets": [ [ 0, 963 ] ] } ]

[ { "id": "407930_T1", "type": "Protein", "text": [ "J chain" ], "offsets": [ [ 27, 34 ] ], "normalized": [] }, { "id": "407930_T2", "type": "Protein", "text": [ "J chain" ], "offsets": [ [ 128, 135 ] ], "normalized": [] }, { "id": "407930_T3", "type": "Protein", "text": [ "J chain" ], "offsets": [ [ 415, 422 ] ], "normalized": [] }, { "id": "407930_T4", "type": "Protein", "text": [ "j chain" ], "offsets": [ [ 586, 593 ] ], "normalized": [] }, { "id": "407930_T6", "type": "Entity", "text": [ "asparagine" ], "offsets": [ [ 670, 680 ] ], "normalized": [] } ]

[ { "id": "407930_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "oligosaccharide structure linked" ], "offsets": [ [ 634, 666 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "407930_T4" }, { "role": "Site", "ref_id": "407930_T6" } ] } ]

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[ { "id": "7014218__text", "type": "abstract", "text": [ "Structural studies on rat prostatic binding protein. The primary structure of its glycosylated component C3. \nThe amino acid sequence of the glycosylated component C3 of rat prostatic binding protein has been determined. The peptides obtained by digestion of the S-carboxamidomethylated or S-aminoethylated glycoprotein with trypsin and Staphylococcus aureus protease were sequenced by manual Edman degradation. The alignment of the fragments was further established with overlapping peptides obtained by enzymic hydrolysis of the modified protein with chymotrypsin and thermolysin, and by chemical cleavage with cyanogen bromide. The glycopeptide C3 contains 77 amino acids corresponding to a molecular weight of 8653. the oligosaccharide chain is attached to the peptide by an N-glycosidic bond to asparagine-17. C3 is an acidic polypeptide due to the presence of ten acidic residues; its three cysteine residues are located at both extremities and in the middle of the molecule. " ], "offsets": [ [ 0, 982 ] ] } ]

[ { "id": "7014218_T1", "type": "Protein", "text": [ "prostatic binding protein" ], "offsets": [ [ 26, 51 ] ], "normalized": [] }, { "id": "7014218_T2", "type": "Protein", "text": [ "prostatic binding protein" ], "offsets": [ [ 174, 199 ] ], "normalized": [] }, { "id": "7014218_T4", "type": "Entity", "text": [ "component C3" ], "offsets": [ [ 95, 107 ] ], "normalized": [] }, { "id": "7014218_T5", "type": "Entity", "text": [ "component C3" ], "offsets": [ [ 154, 166 ] ], "normalized": [] }, { "id": "7014218_T7", "type": "Entity", "text": [ "asparagine-17" ], "offsets": [ [ 800, 813 ] ], "normalized": [] } ]

[ { "id": "7014218_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 82, 94 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7014218_T1" }, { "role": "Site", "ref_id": "7014218_T4" } ] }, { "id": "7014218_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "oligosaccharide chain is attached" ], "offsets": [ [ 724, 757 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7014218_T2" }, { "role": "Site", "ref_id": "7014218_T7" } ] } ]

[ { "id": "7014218_1", "entity_ids": [ "7014218_T2", "7014218_T2" ] } ]

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[ { "id": "3099837__text", "type": "abstract", "text": [ "Complete amino acid sequence of NADPH-cytochrome P-450 reductase from porcine hepatic microsomes. \nThe complete amino acid sequence of porcine hepatic microsomal NADPH-cytochrome P-450 reductase has been determined by microsequence analysis on several sets of proteolytic fragments. Sequence studies were performed initially on a 20-kilodalton (kDa) fragment and then on 80-kDa fragment. The amino-terminal end of the mature protein was blocked with an acetyl group, followed by 676 amino acid residues. It has been revealed that the COOH-terminal 20-kDa fragment has been derived from original enzyme by cleavage at the Asn-Gly (residues 502-503) linkage by an unknown mechanism. An NADPH-protected cysteine residue is located at residue 565, near a region exhibiting high sequence homology with ferredoxin-NADP+ reductase. The FMN and FAD binding regions are possibly located in the amino-terminal region and the middle part of the protein molecule, respectively, as suggested by Porter and Kasper [Porter, T. D., & Kasper, C. B. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 973-977]. When this sequence is compared with that of rat enzyme, 60 amino acid residues are substituted, probably due to species differences. However, total sequence homology between these enzymes is 90%. Hydropathy plot analysis reveals that two regions from residues 27-43 and from residues 523-544 exhibit a high degree of hydrophobicity, suggesting membrane binding or interaction with cytochrome P-450. " ], "offsets": [ [ 0, 1482 ] ] } ]

[ { "id": "3099837_T1", "type": "Protein", "text": [ "NADPH-cytochrome P-450 reductase" ], "offsets": [ [ 32, 64 ] ], "normalized": [] }, { "id": "3099837_T2", "type": "Protein", "text": [ "NADPH-cytochrome P-450 reductas" ], "offsets": [ [ 162, 193 ] ], "normalized": [] }, { "id": "3099837_T3", "type": "Entity", "text": [ "amino-terminal end" ], "offsets": [ [ 392, 410 ] ], "normalized": [] } ]

[ { "id": "3099837_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked with an acetyl group" ], "offsets": [ [ 437, 465 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3099837_T2" }, { "role": "Site", "ref_id": "3099837_T3" } ] } ]

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[ { "id": "6509012__text", "type": "abstract", "text": [ "Purification and sequence of a presynaptic peptide toxin from Conus geographus venom. \nA novel toxin, omega-conotoxin (omega-CgTX), from the venom of the fish-eating marine mollusc Conus geographus has been purified and biochemically characterized. Recently, this omega-conotoxin has been shown to inhibit the voltage-activated entry of Ca2+, thus providing a potentially powerful probe for exploring the vertebrate presynaptic terminal [Kerr, L. M., & Yoshikami, D. (1984) Nature (London) 308, 282-284]. The toxin is a basic 27 amino acid peptide amide with three disulfide bridges. An unusual feature is a remarkable preponderance of hydroxylated amino acids. The sequence of omega-CgTx GVIA is Cys-Lys-Ser- Hyp-Gly5-Ser-Ser-Cys-Ser-Hyp10-Thr-Ser-Tyr-Asn-Cys15-C ys-Arg-Ser- Cys-Asn20-Hyp-Tyr-Thr-Lys-Arg25-Cys-Tyr-NH2. " ], "offsets": [ [ 0, 824 ] ] } ]

[ { "id": "6509012_T1", "type": "Protein", "text": [ "omega-conotoxin" ], "offsets": [ [ 102, 117 ] ], "normalized": [] }, { "id": "6509012_T2", "type": "Protein", "text": [ "omega-CgTX" ], "offsets": [ [ 119, 129 ] ], "normalized": [] }, { "id": "6509012_T3", "type": "Protein", "text": [ "omega-conotoxin" ], "offsets": [ [ 264, 279 ] ], "normalized": [] }, { "id": "6509012_T4", "type": "Protein", "text": [ "omega-CgTx" ], "offsets": [ [ 680, 690 ] ], "normalized": [] }, { "id": "6509012_T6", "type": "Entity", "text": [ "amino acids" ], "offsets": [ [ 650, 661 ] ], "normalized": [] } ]

[ { "id": "6509012_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 637, 649 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6509012_T3" }, { "role": "Site", "ref_id": "6509012_T6" } ] } ]

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[ { "id": "8056893__text", "type": "abstract", "text": [ "Production of overmodified type I procollagen in a case of osteogenesis imperfecta. \nCollagen synthesis in cultured skin fibroblasts from a patient with osteogenesis imperfecta was studied. Approximately 2 fold accumulation of collagen in the cell layer was found. The slower mobility of pro alpha 1 (I) and pro alpha 2 (I) as well as alpha 1 and alpha 2 (I) polypeptide on sodium dodecylsulfate-polyacrylamide gel electrophoresis was detected, indicating that abnormal posttranslational modification could be present in type I procollagen in patient fibroblasts. The degrees of hydroxylation and subsequent glycosylation of lysine residues in the affected collagen were elevated 1.5 and 1.4 fold, respectively. There were no significant changes in the relative content of type III to type I collagen nor the incorporation of mannose into the carboxyterminal propeptide of pro alpha 1 (I) and pro alpha 2 (I). These results indicate that the patient produces an over-modified type I procollagen which is responsible for the clinical features and has a collagen abnormality already reported in type II osteogenesis imperfecta. " ], "offsets": [ [ 0, 1126 ] ] } ]

[ { "id": "8056893_T1", "type": "Protein", "text": [ "type I procollagen" ], "offsets": [ [ 27, 45 ] ], "normalized": [] }, { "id": "8056893_T2", "type": "Protein", "text": [ "Collagen" ], "offsets": [ [ 85, 93 ] ], "normalized": [] }, { "id": "8056893_T3", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 227, 235 ] ], "normalized": [] }, { "id": "8056893_T4", "type": "Protein", "text": [ " alpha 1 (I)" ], "offsets": [ [ 291, 303 ] ], "normalized": [] }, { "id": "8056893_T5", "type": "Protein", "text": [ "alpha 2 (I)" ], "offsets": [ [ 312, 323 ] ], "normalized": [] }, { "id": "8056893_T6", "type": "Protein", "text": [ "alpha 1" ], "offsets": [ [ 335, 342 ] ], "normalized": [] }, { "id": "8056893_T7", "type": "Protein", "text": [ "alpha 2 (I)" ], "offsets": [ [ 347, 358 ] ], "normalized": [] }, { "id": "8056893_T8", "type": "Protein", "text": [ "type I procollagen" ], "offsets": [ [ 521, 539 ] ], "normalized": [] }, { "id": "8056893_T9", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 657, 665 ] ], "normalized": [] }, { "id": "8056893_T10", "type": "Protein", "text": [ "type III" ], "offsets": [ [ 773, 781 ] ], "normalized": [] }, { "id": "8056893_T11", "type": "Protein", "text": [ "type I collagen" ], "offsets": [ [ 785, 800 ] ], "normalized": [] }, { "id": "8056893_T12", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 877, 888 ] ], "normalized": [] }, { "id": "8056893_T13", "type": "Protein", "text": [ "alpha 2 (I)" ], "offsets": [ [ 897, 908 ] ], "normalized": [] }, { "id": "8056893_T14", "type": "Protein", "text": [ "type I procollagen" ], "offsets": [ [ 976, 994 ] ], "normalized": [] }, { "id": "8056893_T15", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 1052, 1060 ] ], "normalized": [] }, { "id": "8056893_T18", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 625, 631 ] ], "normalized": [] } ]

[ { "id": "8056893_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 579, 592 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8056893_T9" }, { "role": "Site", "ref_id": "8056893_T18" } ] }, { "id": "8056893_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 608, 621 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8056893_T9" }, { "role": "Site", "ref_id": "8056893_T18" } ] } ]

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[ { "id": "1350932__text", "type": "abstract", "text": [ "cDNA, amino acid and carbohydrate sequence of barley seed-specific peroxidase BP 1. \nThe major peroxidase of barley seed BP 1 was characterized. Previous studies showed a low carbohydrate content, low specific activity and tissue-specific expression, and suggested that this basic peroxidase could be particularly useful in the elucidation of the structure-function relationship and in the study of the biological roles of plant peroxidases (S.K. Rasmussen, K.G. Welinder and J. Hejgaard (1991) Plant Mol Biol 16: 317-327). A cDNA library was prepared from mRNA isolated from seeds 15 days after flowering. Full-length clones were obtained and showed 3' end length variants, a G+C content of 69% in the translated region, a 90% G or C preference in the wobble position of the codons and a typical signal peptide sequence. N-terminal amino acid sequencing and sequence analysis of tryptic peptides verified 98% of the sequence of the mature BP 1 which contains 309 amino acid residues. BP 1 is the first characterized plant peroxidase which is not blocked by pyroglutamate. BP 1 polymorphism was observed. BP 1 is less than 50% identical to other plant peroxidases which, taken together with its developmentally dependent expression in the endosperm 15-20 days after flowering, suggests a unique biological role of this enzyme. The barley peroxidase is processed at the C-terminus and might be targeted to the vacuole. The single site of glycosylation is located near the C-terminus in the N-glycosylation sequon -Asn-Cys-Ser- in which Cys forms part of a disulphide bridge. The major glycan is a typical plant modified-type structure, Man alpha 1-6(Xyl beta 1-2)Man beta 1-4GlcNAc beta 1-4(Fuc alpha 1-3)GlcNAc. The BP 1 gene was RFLP-mapped on barley chromosome 3, and we propose Prx5 as the name for this new peroxidase locus. " ], "offsets": [ [ 0, 1829 ] ] } ]

[ { "id": "1350932_T1", "type": "Protein", "text": [ "BP 1" ], "offsets": [ [ 78, 82 ] ], "normalized": [] }, { "id": "1350932_T2", "type": "Protein", "text": [ "BP 1" ], "offsets": [ [ 121, 125 ] ], "normalized": [] }, { "id": "1350932_T3", "type": "Protein", "text": [ "BP 1" ], "offsets": [ [ 940, 944 ] ], "normalized": [] }, { "id": "1350932_T4", "type": "Protein", "text": [ "BP 1" ], "offsets": [ [ 985, 989 ] ], "normalized": [] }, { "id": "1350932_T5", "type": "Protein", "text": [ "BP 1" ], "offsets": [ [ 1073, 1077 ] ], "normalized": [] }, { "id": "1350932_T6", "type": "Protein", "text": [ "BP 1" ], "offsets": [ [ 1105, 1109 ] ], "normalized": [] }, { "id": "1350932_T7", "type": "Protein", "text": [ "BP 1" ], "offsets": [ [ 1716, 1720 ] ], "normalized": [] }, { "id": "1350932_T9", "type": "Entity", "text": [ "Cys" ], "offsets": [ [ 1535, 1538 ] ], "normalized": [] } ]

[ { "id": "1350932_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "single site of glycosylation is located" ], "offsets": [ [ 1422, 1461 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1350932_T6" }, { "role": "Site", "ref_id": "1350932_T9" } ] } ]

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

[ { "id": "8226858_T1", "type": "Protein", "text": [ "coagulation factors IX" ], "offsets": [ [ 100, 122 ] ], "normalized": [] }, { "id": "8226858_T2", "type": "Protein", "text": [ "X" ], "offsets": [ [ 127, 128 ] ], "normalized": [] }, { "id": "8226858_T3", "type": "Protein", "text": [ "coagulation factors IX" ], "offsets": [ [ 589, 611 ] ], "normalized": [] }, { "id": "8226858_T4", "type": "Protein", "text": [ "X" ], "offsets": [ [ 616, 617 ] ], "normalized": [] }, { "id": "8226858_T5", "type": "Protein", "text": [ "factor X" ], "offsets": [ [ 1053, 1061 ] ], "normalized": [] }, { "id": "8226858_T6", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 1157, 1166 ] ], "normalized": [] }, { "id": "8226858_T7", "type": "Entity", "text": [ "aspartate" ], "offsets": [ [ 14, 23 ] ], "normalized": [] }, { "id": "8226858_T10", "type": "Entity", "text": [ "aspartic acid" ], "offsets": [ [ 148, 161 ] ], "normalized": [] }, { "id": "8226858_T11", "type": "Entity", "text": [ "erythro-beta-aspartic acid" ], "offsets": [ [ 165, 191 ] ], "normalized": [] }, { "id": "8226858_T12", "type": "Entity", "text": [ "Hya" ], "offsets": [ [ 193, 196 ] ], "normalized": [] }, { "id": "8226858_T13", "type": "Entity", "text": [ "consensus sequence" ], "offsets": [ [ 344, 362 ] ], "normalized": [] } ]

[ { "id": "8226858_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 24, 37 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T1" }, { "role": "Site", "ref_id": "8226858_T7" } ] }, { "id": "8226858_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 24, 37 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T2" }, { "role": "Site", "ref_id": "8226858_T7" } ] }, { "id": "8226858_E3", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "Hydroxylation" ], "offsets": [ [ 131, 144 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T2" }, { "role": "Site", "ref_id": "8226858_T10" } ] }, { "id": "8226858_E4", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "Hydroxylation" ], "offsets": [ [ 131, 144 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T1" }, { "role": "Site", "ref_id": "8226858_T10" } ] }, { "id": "8226858_E5", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 367, 380 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T2" }, { "role": "Site", "ref_id": "8226858_T13" } ] }, { "id": "8226858_E6", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 367, 380 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T1" }, { "role": "Site", "ref_id": "8226858_T13" } ] }, { "id": "8226858_E7", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "beta-hydroxylated" ], "offsets": [ [ 674, 691 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T3" } ] }, { "id": "8226858_E8", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "beta-hydroxylated" ], "offsets": [ [ 674, 691 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T4" } ] }, { "id": "8226858_E9", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "non-beta-hydroxylated" ], "offsets": [ [ 700, 721 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T4" } ] }, { "id": "8226858_E10", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "non-beta-hydroxylated" ], "offsets": [ [ 700, 721 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T3" } ] }, { "id": "8226858_E11", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 1020, 1032 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T5" } ] }, { "id": "8226858_E12", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "nonhydroxylated" ], "offsets": [ [ 1037, 1052 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T5" } ] }, { "id": "8226858_E13", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1177, 1190 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8226858_T6" } ] } ]

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[ { "id": "17327272__text", "type": "abstract", "text": [ "Epigenetic regulation of facultative heterochromatinisation in Planococcus citri via the Me(3)K9H3-HP1-Me(3)K20H4 pathway. \nUsing RNA interference (RNAi) we have conducted a functional analysis of the HP1-like chromobox gene pchet2 during embryogenesis of the mealybug Planococcus citri. Knocking down pchet2 expression results in decondensation of the male-specific chromocenter that normally arises from the developmentally-regulated facultative heterochromatinisation of the paternal chromosome complement. Together with the disappearance of the chromocenter the staining levels of two associated histone modifications, tri-methylated lysine 9 of histone H3 [Me(3)K9H3] and tri-methylated lysine 20 of histone H4 [Me(3)K20H4], are reduced to undetectable levels. Embryos treated with double-stranded RNA (dsRNA) targeting pchet2 also exhibit chromosome abnormalities, such as aberrant chromosome condensation, and also the presence of metaphases that contain 'lagging' chromosomes. We conclude that PCHET2 regulates chromosome behavior during metaphase and is a crucial component of a Me(3)K9H3-HP1-Me(3)K20H4 pathway involved in the facultative heterochromatinisation of the (imprinted) paternal chromosome set. " ], "offsets": [ [ 0, 1216 ] ] } ]

[ { "id": "17327272_T1", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 96, 98 ] ], "normalized": [] }, { "id": "17327272_T2", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 111, 113 ] ], "normalized": [] }, { "id": "17327272_T3", "type": "Protein", "text": [ "pchet2" ], "offsets": [ [ 225, 231 ] ], "normalized": [] }, { "id": "17327272_T4", "type": "Protein", "text": [ "pchet2" ], "offsets": [ [ 302, 308 ] ], "normalized": [] }, { "id": "17327272_T5", "type": "Protein", "text": [ "histone H3" ], "offsets": [ [ 650, 660 ] ], "normalized": [] }, { "id": "17327272_T6", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 669, 671 ] ], "normalized": [] }, { "id": "17327272_T7", "type": "Protein", "text": [ "histone H4" ], "offsets": [ [ 705, 715 ] ], "normalized": [] }, { "id": "17327272_T8", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 725, 727 ] ], "normalized": [] }, { "id": "17327272_T9", "type": "Protein", "text": [ "pchet2" ], "offsets": [ [ 825, 831 ] ], "normalized": [] }, { "id": "17327272_T10", "type": "Protein", "text": [ "PCHET2" ], "offsets": [ [ 1002, 1008 ] ], "normalized": [] }, { "id": "17327272_T11", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 1095, 1097 ] ], "normalized": [] }, { "id": "17327272_T12", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1110, 1112 ] ], "normalized": [] }, { "id": "17327272_T14", "type": "Entity", "text": [ "lysine 9" ], "offsets": [ [ 638, 646 ] ], "normalized": [] }, { "id": "17327272_T16", "type": "Entity", "text": [ "lysine 20" ], "offsets": [ [ 692, 701 ] ], "normalized": [] } ]

[ { "id": "17327272_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "tri-methylated" ], "offsets": [ [ 623, 637 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "17327272_T5" }, { "role": "Site", "ref_id": "17327272_T14" } ] }, { "id": "17327272_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "tri-methylated" ], "offsets": [ [ 677, 691 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "17327272_T7" }, { "role": "Site", "ref_id": "17327272_T16" } ] } ]

[ { "id": "17327272_1", "entity_ids": [ "17327272_T5", "17327272_T6" ] }, { "id": "17327272_2", "entity_ids": [ "17327272_T7", "17327272_T8" ] } ]

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[ { "id": "3182782__text", "type": "abstract", "text": [ "Purification and identification of [hydroxyprolyl3]bradykinin in ascitic fluid from a patient with gastric cancer. \nKinins in the ascitic fluid from a patient with gastric cancer were purified by gel filtration and reversed-phase high-performance liquid chromatography (HPLC). Two fractions (fractions I and II) showed kinin activity. Fraction I did not correspond to either bradykinin or other known kinins, whereas fraction II corresponded to bradykinin. Fraction I contained 8 amino acid residues from bradykinin minus 1 proline plus 1 additional hydroxyproline. Sequence analysis of fraction I showed that the proline at the third amino acid residue of bradykinin was replaced by hydroxyproline. The retention time of fraction I on reversed-phase HPLC was exactly the same as that of synthetic [hydroxyprolyl3]bradykinin (Arg-Pro-Hyp-Gly-Phe-Ser-Pro-Phe-Arg) and was distinguishable from des-Pro3-bradykinin. Thus, these results demonstrate for the first time the presence of [hydroxyprolyl3]bradykinin in vivo. This is also the first report of the presence of bradykinin in human tumor ascites. " ], "offsets": [ [ 0, 1100 ] ] } ]

[ { "id": "3182782_T1", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 51, 61 ] ], "normalized": [] }, { "id": "3182782_T2", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 445, 455 ] ], "normalized": [] }, { "id": "3182782_T3", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 505, 515 ] ], "normalized": [] }, { "id": "3182782_T4", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 657, 667 ] ], "normalized": [] }, { "id": "3182782_T5", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 814, 824 ] ], "normalized": [] }, { "id": "3182782_T6", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 901, 911 ] ], "normalized": [] }, { "id": "3182782_T7", "type": "Protein", "text": [ "bradykinin" ], "offsets": [ [ 996, 1006 ] ], "normalized": [] }, { "id": "3182782_T8", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 614, 621 ] ], "normalized": [] } ]

[ { "id": "3182782_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "replaced by hydroxyproline" ], "offsets": [ [ 672, 698 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3182782_T4" }, { "role": "Site", "ref_id": "3182782_T8" } ] } ]

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[ { "id": "2928307__text", "type": "abstract", "text": [ "Post-translational modifications in the large subunit of ribulose bisphosphate carboxylase/oxygenase. \nTwo adjacent N-terminal tryptic peptides of the large subunit of ribulose bisphosphate carboxylase/oxygenase [3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39] from spinach, wheat, tobacco, and muskmelon were removed by limited tryptic proteolysis. Characterization by peptide sequencing, amino acid composition, and tandem mass spectrometry revealed that the N-terminal residue from the large subunit of the enzyme from each plant species was acetylated proline. The sequence of the penultimate N-terminal tryptic peptide from the large subunit of the spinach and wheat enzyme was consistent with previous primary structure determinations. However, the penultimate N-terminal peptide from the large subunit of both the tobacco and muskmelon enzymes, while identical, differed from the corresponding peptide from spinach and wheat by containing a trimethyllysyl residue at position 14. Thus, tryptic proteolysis occurred at lysine-18 rather than lysine-14 as with the spinach and wheat enzymes. A comparison of the DNA sequences for the large subunit of ribulose bisphosphate carboxylase/oxygenase indicates that the N terminus has been post-translationally processed by removal of methionine-1 and serine-2 followed by acetylation of proline-3. In addition, for the enzyme from tobacco and muskmelon a third post-translational modification occurs at lysine-14 in the form of N epsilon-trimethylation. " ], "offsets": [ [ 0, 1518 ] ] } ]

[ { "id": "2928307_T1", "type": "Protein", "text": [ "ribulose bisphosphate" ], "offsets": [ [ 57, 78 ] ], "normalized": [] }, { "id": "2928307_T2", "type": "Protein", "text": [ "ribulose bisphosphate carboxylase/oxygenase" ], "offsets": [ [ 168, 211 ] ], "normalized": [] }, { "id": "2928307_T3", "type": "Protein", "text": [ "3-phospho-D-glycerate carboxy-lyase" ], "offsets": [ [ 213, 248 ] ], "normalized": [] }, { "id": "2928307_T4", "type": "Protein", "text": [ "ribulose bisphosphate" ], "offsets": [ [ 1170, 1191 ] ], "normalized": [] }, { "id": "2928307_T6", "type": "Entity", "text": [ "proline" ], "offsets": [ [ 571, 578 ] ], "normalized": [] }, { "id": "2928307_T8", "type": "Entity", "text": [ "proline-3" ], "offsets": [ [ 1351, 1360 ] ], "normalized": [] }, { "id": "2928307_T9", "type": "Entity", "text": [ "lysine-14" ], "offsets": [ [ 1467, 1476 ] ], "normalized": [] } ]

[ { "id": "2928307_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 560, 570 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2928307_T2" }, { "role": "Site", "ref_id": "2928307_T6" } ] }, { "id": "2928307_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 1336, 1347 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2928307_T4" }, { "role": "Site", "ref_id": "2928307_T8" } ] }, { "id": "2928307_E3", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "N epsilon-trimethylation" ], "offsets": [ [ 1492, 1516 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2928307_T4" }, { "role": "Site", "ref_id": "2928307_T9" } ] } ]

[ { "id": "2928307_1", "entity_ids": [ "2928307_T2", "2928307_T3" ] } ]

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[ { "id": "8753789__text", "type": "abstract", "text": [ "Molecular cloning, sequencing, and heterologous expression of a novel zinc-containing ferredoxin gene from a thermoacidophilic Archaeon Sulfolobus sp. strain 7. \nThe gene encoding a novel zinc-containing ferredoxin from a hyperthermophilic and acidophilic archaeon (archaebacterium) Sulfolobus sp. strain 7 was cloned and sequenced. The DNA sequence predicts a 103 residue protein after removal of N-terminal methionine, which is in good agreement with the results of the protein analysis. Surprisingly, the residues responsible for binding a zinc atom were conserved among three other thermoacidophilic archaea. A common sequence stretch VXGXHXGHX8-17PXXLGXHGTX38-56KXDPV is proposed as a new zinc-binding motif, where three histidines and an aspartic acid are ligated to a zinc atom. The ferredoxin gene was expressed in Eschericia coli. The recombinant ferredoxin was indistinguishable from the protein purified from Sulfolobus sp. strain 7 cells by several criteria so far investigated except that the methylation of the 29th lysine was suppressed. " ], "offsets": [ [ 0, 1058 ] ] } ]

[ { "id": "8753789_T1", "type": "Protein", "text": [ "ferredoxin" ], "offsets": [ [ 86, 96 ] ], "normalized": [] }, { "id": "8753789_T2", "type": "Protein", "text": [ "ferredoxin" ], "offsets": [ [ 204, 214 ] ], "normalized": [] }, { "id": "8753789_T3", "type": "Protein", "text": [ "ferredoxin" ], "offsets": [ [ 794, 804 ] ], "normalized": [] }, { "id": "8753789_T4", "type": "Protein", "text": [ "ferredoxin" ], "offsets": [ [ 861, 871 ] ], "normalized": [] }, { "id": "8753789_T6", "type": "Entity", "text": [ "29th lysine" ], "offsets": [ [ 1030, 1041 ] ], "normalized": [] } ]

[ { "id": "8753789_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1011, 1022 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "8753789_T4" }, { "role": "Site", "ref_id": "8753789_T6" } ] } ]

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[ { "id": "15659401__text", "type": "abstract", "text": [ "Characterization of the yeast trimeric-SAS acetyltransferase complex. \nThe yeast SAS2 (Something About Silencing 2) gene encodes a member of the MYST protein family of histone acetyltransferases (HATs) and is involved in transcriptional silencing at all silent loci (HML, HMR, telomeres, and rDNA) in Saccharomyces cerevisiae. Sas2 is the catalytic subunit of a yeast histone acetyltransferase complex termed SAS complex. The enzymatic activity of SAS complex on free histones has been reported, but nucleosomal HAT activity has not yet been documented. Here we show that the native yeast SAS complex is a small trimeric protein complex composed solely of Sas2, Sas4, and Sas5 with a molecular mass of about 125 kDa. It is capable of acetylating both free histones and nucleosomes, although the nucleosomal HAT activity of SAS complex is very weak when compared with that of NuA4, the other member of MYST HAT complex. We also demonstrate that the putative acetyl CoA binding motif in Sas2 is essential for both the in vivo silencing function and the enzymatic activity of SAS complex. Unlike NuA4, which acetylates all four available lysines at the N-terminal tail of histone H4, SAS complex exclusively acetylates lysine 16 of histone H4 in vitro and is required for the bulk of H4 lysine 16 acetylation in vivo. This specific lysine preference corresponds to the role of SAS complex in antagonizing the spreading of Sir proteins at silent loci in S. cerevisiae. " ], "offsets": [ [ 0, 1465 ] ] } ]

[ { "id": "15659401_T1", "type": "Protein", "text": [ "SAS2" ], "offsets": [ [ 81, 85 ] ], "normalized": [] }, { "id": "15659401_T2", "type": "Protein", "text": [ "Something About Silencing 2" ], "offsets": [ [ 87, 114 ] ], "normalized": [] }, { "id": "15659401_T3", "type": "Protein", "text": [ "Sas2" ], "offsets": [ [ 327, 331 ] ], "normalized": [] }, { "id": "15659401_T4", "type": "Protein", "text": [ "Sas2" ], "offsets": [ [ 656, 660 ] ], "normalized": [] }, { "id": "15659401_T5", "type": "Protein", "text": [ "Sas4" ], "offsets": [ [ 662, 666 ] ], "normalized": [] }, { "id": "15659401_T6", "type": "Protein", "text": [ "Sas5" ], "offsets": [ [ 672, 676 ] ], "normalized": [] }, { "id": "15659401_T7", "type": "Protein", "text": [ "Sas2" ], "offsets": [ [ 985, 989 ] ], "normalized": [] }, { "id": "15659401_T8", "type": "Protein", "text": [ "histone H4" ], "offsets": [ [ 1169, 1179 ] ], "normalized": [] }, { "id": "15659401_T9", "type": "Protein", "text": [ "histone H4" ], "offsets": [ [ 1229, 1239 ] ], "normalized": [] }, { "id": "15659401_T10", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1281, 1283 ] ], "normalized": [] }, { "id": "15659401_T12", "type": "Entity", "text": [ "lysine 16" ], "offsets": [ [ 1216, 1225 ] ], "normalized": [] }, { "id": "15659401_T13", "type": "Entity", "text": [ "lysine 16" ], "offsets": [ [ 1284, 1293 ] ], "normalized": [] } ]

[ { "id": "15659401_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylates" ], "offsets": [ [ 1105, 1115 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15659401_T9" }, { "role": "Site", "ref_id": "15659401_T12" } ] }, { "id": "15659401_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 1294, 1305 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15659401_T10" }, { "role": "Site", "ref_id": "15659401_T13" } ] } ]

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[ { "id": "4086472__text", "type": "abstract", "text": [ "Amino acid sequence of calmodulin from wheat germ. \nThe complete amino acid sequence of calmodulin from wheat germ was determined by isolating and sequencing the cyanogen bromide and tryptic peptides. The protein consisted of 149 amino acid residues and its amino(N)-terminus was blocked with an acetyl group. Wheat germ calmodulin lacked tryptophan and contained 1 mol each of histidine, tyrosine, cysteine, and N epsilon-trimethyllysine residues per mol of the protein. A comparison of its amino acid sequence with that of bovine brain calmodulin indicated that there were eleven amino acid subsitutions other than amide assignments, two insertions and one deletion of amino acid residues in wheat germ calmodulin. " ], "offsets": [ [ 0, 717 ] ] } ]

[ { "id": "4086472_T1", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 23, 33 ] ], "normalized": [] }, { "id": "4086472_T2", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 88, 98 ] ], "normalized": [] }, { "id": "4086472_T3", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 321, 331 ] ], "normalized": [] }, { "id": "4086472_T4", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 538, 548 ] ], "normalized": [] }, { "id": "4086472_T5", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 705, 715 ] ], "normalized": [] }, { "id": "4086472_T6", "type": "Entity", "text": [ "amino(N)-terminus" ], "offsets": [ [ 258, 275 ] ], "normalized": [] } ]

[ { "id": "4086472_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked with an acetyl group" ], "offsets": [ [ 280, 308 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "4086472_T2" }, { "role": "Site", "ref_id": "4086472_T6" } ] } ]

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[ { "id": "1939027__text", "type": "abstract", "text": [ "The primary structure of skeletal muscle myosin heavy chain: I. Sequence of the amino-terminal 23 kDa fragment. \nSubfragment-1 was prepared from adult chicken pectoralis myosin by limited digestion with alpha-chymotrypsin, and an amino-terminal 23 kDa fragment of the heavy chain was obtained by digesting the subfragment-1 with trypsin. The 205-residue sequence of the fragment was determined by sequencing its cyanogen bromide, tryptic, and chymotryptic peptides. The amino-terminal alpha-amino group of the fragment was acetylated, and two methylated lysines; epsilon-N-monomethyllysine and epsilon-N-trimethyllysine were recognized at the 35th and 130th positions, respectively, as in rabbit skeletal myosin. Comparing the 205-residue sequence of the skeletal myosin with those of cardiac, and gizzard myosins from chicken, considerable differences are recognized, especially in the amino-terminal region, but strong homologies are observed around the reactive lysine residue, around the epsilon-N-trimethyllysine residue, and around the consensus sequence of GXXGXGKT for nucleotide-binding proteins. On the other hand, only 12 amino acid substitutions are recognized between adult and embryonic skeletal myosins, allowing for the post-translational methylation. " ], "offsets": [ [ 0, 1268 ] ] } ]

[ { "id": "1939027_T1", "type": "Protein", "text": [ "myosin heavy chain" ], "offsets": [ [ 41, 59 ] ], "normalized": [] }, { "id": "1939027_T2", "type": "Protein", "text": [ "myosin" ], "offsets": [ [ 705, 711 ] ], "normalized": [] }, { "id": "1939027_T3", "type": "Protein", "text": [ "myosin" ], "offsets": [ [ 764, 770 ] ], "normalized": [] }, { "id": "1939027_T4", "type": "Protein", "text": [ "myosins" ], "offsets": [ [ 806, 813 ] ], "normalized": [] }, { "id": "1939027_T5", "type": "Protein", "text": [ "myosins" ], "offsets": [ [ 1210, 1217 ] ], "normalized": [] }, { "id": "1939027_T6", "type": "Entity", "text": [ "amino-terminal alpha-amino group" ], "offsets": [ [ 470, 502 ] ], "normalized": [] }, { "id": "1939027_T9", "type": "Entity", "text": [ "lysines" ], "offsets": [ [ 554, 561 ] ], "normalized": [] } ]

[ { "id": "1939027_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 523, 533 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1939027_T2" }, { "role": "Site", "ref_id": "1939027_T6" } ] }, { "id": "1939027_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 543, 553 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1939027_T2" }, { "role": "Site", "ref_id": "1939027_T9" } ] }, { "id": "1939027_E3", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "post-translational methylation" ], "offsets": [ [ 1236, 1266 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1939027_T5" } ] } ]

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[ { "id": "2993260__text", "type": "abstract", "text": [ "Amino acid sequence of acylphosphatase from rabbit skeletal muscle. \nThe complete amino acid sequence of acylphosphatase from rabbit skeletal muscle has been elucidated by automatic Edman degradation of peptides obtained from staphylococcal protease and trypsin digestions. The enzyme consisted of a single polypeptide chain of 98 amino acid residues, lacking only histidine. Its amino (N)-terminus was blocked by an acetyl group. The presented sequence of rabbit muscle enzyme was compared with those of equine and porcine muscle enzymes. There were four unique replacements, i.e., Arg-4, Asp-28, Arg-31, and Glu-56 in the sequences of both equine and porcine muscle enzymes were replaced by Gly, Gly, Lys, and Asp, respectively, in that of rabbit muscle enzyme. Extensive structural homology was observed among the three enzymes. " ], "offsets": [ [ 0, 832 ] ] } ]

[ { "id": "2993260_T1", "type": "Protein", "text": [ "acylphosphatase" ], "offsets": [ [ 23, 38 ] ], "normalized": [] }, { "id": "2993260_T2", "type": "Protein", "text": [ "acylphosphatase" ], "offsets": [ [ 105, 120 ] ], "normalized": [] }, { "id": "2993260_T3", "type": "Entity", "text": [ "amino (N)-terminus" ], "offsets": [ [ 380, 398 ] ], "normalized": [] } ]

[ { "id": "2993260_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocked by an acetyl group" ], "offsets": [ [ 403, 429 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2993260_T2" }, { "role": "Site", "ref_id": "2993260_T3" } ] } ]

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[ { "id": "19516333__text", "type": "abstract", "text": [ "Histone H4 lysine 16 acetylation regulates cellular lifespan. \nCells undergoing developmental processes are characterized by persistent non-genetic alterations in chromatin, termed epigenetic changes, represented by distinct patterns of DNA methylation and histone post-translational modifications. Sirtuins, a group of conserved NAD(+)-dependent deacetylases or ADP-ribosyltransferases, promote longevity in diverse organisms; however, their molecular mechanisms in ageing regulation remain poorly understood. Yeast Sir2, the first member of the family to be found, establishes and maintains chromatin silencing by removing histone H4 lysine 16 acetylation and bringing in other silencing proteins. Here we report an age-associated decrease in Sir2 protein abundance accompanied by an increase in H4 lysine 16 acetylation and loss of histones at specific subtelomeric regions in replicatively old yeast cells, which results in compromised transcriptional silencing at these loci. Antagonizing activities of Sir2 and Sas2, a histone acetyltransferase, regulate the replicative lifespan through histone H4 lysine 16 at subtelomeric regions. This pathway, distinct from existing ageing models for yeast, may represent an evolutionarily conserved function of sirtuins in regulation of replicative ageing by maintenance of intact telomeric chromatin. " ], "offsets": [ [ 0, 1347 ] ] } ]

[ { "id": "19516333_T1", "type": "Protein", "text": [ "Histone H4" ], "offsets": [ [ 0, 10 ] ], "normalized": [] }, { "id": "19516333_T2", "type": "Protein", "text": [ "Sir2" ], "offsets": [ [ 517, 521 ] ], "normalized": [] }, { "id": "19516333_T3", "type": "Protein", "text": [ "histone H4" ], "offsets": [ [ 625, 635 ] ], "normalized": [] }, { "id": "19516333_T4", "type": "Protein", "text": [ "Sir2" ], "offsets": [ [ 745, 749 ] ], "normalized": [] }, { "id": "19516333_T5", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 798, 800 ] ], "normalized": [] }, { "id": "19516333_T6", "type": "Protein", "text": [ "Sir2" ], "offsets": [ [ 1008, 1012 ] ], "normalized": [] }, { "id": "19516333_T7", "type": "Protein", "text": [ "Sas2" ], "offsets": [ [ 1017, 1021 ] ], "normalized": [] }, { "id": "19516333_T8", "type": "Entity", "text": [ "lysine 16" ], "offsets": [ [ 11, 20 ] ], "normalized": [] }, { "id": "19516333_T10", "type": "Entity", "text": [ "lysine 16" ], "offsets": [ [ 636, 645 ] ], "normalized": [] }, { "id": "19516333_T12", "type": "Entity", "text": [ "lysine 16" ], "offsets": [ [ 801, 810 ] ], "normalized": [] } ]

[ { "id": "19516333_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 21, 32 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "19516333_T1" }, { "role": "Site", "ref_id": "19516333_T8" } ] }, { "id": "19516333_E2", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 646, 657 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "19516333_T3" }, { "role": "Site", "ref_id": "19516333_T10" } ] }, { "id": "19516333_E3", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 811, 822 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "19516333_T5" }, { "role": "Site", "ref_id": "19516333_T12" } ] } ]

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[ { "id": "3298225__text", "type": "abstract", "text": [ "A second type of protein methylation reaction in bacterial chemotaxis. \nCheZ is the product of one of six genes required for sensory processing in Escherichia coli and Salmonella typhimurium chemotaxis. This 24-kDa cytoplasmic protein is modified by a posttranslational methylation reaction. The modified residue has been identified by analysis of radioactively labeled protein from two-dimensional electrophoretograms and Edman degradation of CheZ protein isolated by immunoaffinity chromatography using anti-CheZ monoclonal antibodies. The methylated group is an N-monomethylmethionine residue at the amino terminus of CheZ. L16, a ribosomal protein that is required for peptidyltransferase activity during protein synthesis, is also methylated at its amino-terminal methionine (Chen, R., Brosius, J., and Wittmann-Liebold, B. (1977) J. Mol. Biol. 111, 173-181). Homologous sequences at the amino termini of L16 and CheZ raise the possibility that a single S-adenosylmethionine-dependent methyltransferase modifies both proteins. " ], "offsets": [ [ 0, 1036 ] ] } ]

[ { "id": "3298225_T1", "type": "Protein", "text": [ "CheZ" ], "offsets": [ [ 72, 76 ] ], "normalized": [] }, { "id": "3298225_T2", "type": "Protein", "text": [ "CheZ" ], "offsets": [ [ 446, 450 ] ], "normalized": [] }, { "id": "3298225_T3", "type": "Protein", "text": [ "CheZ" ], "offsets": [ [ 512, 516 ] ], "normalized": [] }, { "id": "3298225_T4", "type": "Protein", "text": [ "CheZ" ], "offsets": [ [ 624, 628 ] ], "normalized": [] }, { "id": "3298225_T5", "type": "Protein", "text": [ "L16" ], "offsets": [ [ 630, 633 ] ], "normalized": [] }, { "id": "3298225_T6", "type": "Protein", "text": [ "peptidyltransferase" ], "offsets": [ [ 676, 695 ] ], "normalized": [] }, { "id": "3298225_T7", "type": "Protein", "text": [ "L16" ], "offsets": [ [ 914, 917 ] ], "normalized": [] }, { "id": "3298225_T8", "type": "Protein", "text": [ "CheZ" ], "offsets": [ [ 922, 926 ] ], "normalized": [] }, { "id": "3298225_T10", "type": "Entity", "text": [ "N-monomethylmethionine" ], "offsets": [ [ 568, 590 ] ], "normalized": [] }, { "id": "3298225_T12", "type": "Entity", "text": [ "methionine" ], "offsets": [ [ 772, 782 ] ], "normalized": [] } ]

[ { "id": "3298225_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 545, 555 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3298225_T4" }, { "role": "Site", "ref_id": "3298225_T10" } ] }, { "id": "3298225_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 739, 749 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3298225_T6" }, { "role": "Site", "ref_id": "3298225_T12" } ] } ]

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[ { "id": "2376577__text", "type": "abstract", "text": [ "The covalent structure of Acanthamoeba actobindin. \nActobindin is a protein from Acanthamoeba castellanii with bivalent affinity for monomeric actin. Because it can bind two molecules of actin, actobindin is a substantially more potent inhibitor of the early phase of actin polymerization than of F-actin elongation. The complete amino acid sequence of 88 residues has been deduced from the determined sequences of overlapping peptides obtained by cleavage with trypsin, Staphylococcus V8 protease, endoproteinase Asp-N, and CNBr. Actobindin contains 2 trimethyllysine residues and an acetylated NH2 terminus. About 76% of the actobindin molecule consists of two nearly identical repeated segments of approximately 33 residues each. This could explain actobindin's bivalent affinity for actin. The circular dichroism spectrum of actobindin is consistent with 15% alpha-helix and 22% beta-sheet structure. A hexapeptide with sequence LKHAET, which occurs at the beginning of each of the repeated segments of actobindin, is very similar to sequences found in tropomyosin, muscle myosin heavy chain, paramyosin, and Dictyostelium alpha-actinin. A longer stretch in each repeated segment is similar to sequences in mammalian and amoeba profilins. Interestingly, the sequences around the trimethyllysine residues in each of the repeats are similar to the sequences flanking the trimethyllysine residue of rabbit reticulocyte elongation factor 1 alpha, but not to the sequences around the trimethyllysine residues in Acanthamoeba actin and Acanthamoeba profilins I and II. " ], "offsets": [ [ 0, 1567 ] ] } ]

[ { "id": "2376577_T1", "type": "Protein", "text": [ "actobindin" ], "offsets": [ [ 39, 49 ] ], "normalized": [] }, { "id": "2376577_T2", "type": "Protein", "text": [ "Actobindin" ], "offsets": [ [ 52, 62 ] ], "normalized": [] }, { "id": "2376577_T3", "type": "Protein", "text": [ "actin" ], "offsets": [ [ 143, 148 ] ], "normalized": [] }, { "id": "2376577_T4", "type": "Protein", "text": [ "actin" ], "offsets": [ [ 187, 192 ] ], "normalized": [] }, { "id": "2376577_T5", "type": "Protein", "text": [ "actobindin" ], "offsets": [ [ 194, 204 ] ], "normalized": [] }, { "id": "2376577_T6", "type": "Protein", "text": [ "F-actin" ], "offsets": [ [ 297, 304 ] ], "normalized": [] }, { "id": "2376577_T7", "type": "Protein", "text": [ "V8 protease" ], "offsets": [ [ 486, 497 ] ], "normalized": [] }, { "id": "2376577_T8", "type": "Protein", "text": [ "Actobindin" ], "offsets": [ [ 531, 541 ] ], "normalized": [] }, { "id": "2376577_T9", "type": "Protein", "text": [ "actin" ], "offsets": [ [ 787, 792 ] ], "normalized": [] }, { "id": "2376577_T10", "type": "Protein", "text": [ "actobindin" ], "offsets": [ [ 1007, 1017 ] ], "normalized": [] }, { "id": "2376577_T11", "type": "Protein", "text": [ "tropomyosin" ], "offsets": [ [ 1057, 1068 ] ], "normalized": [] }, { "id": "2376577_T12", "type": "Protein", "text": [ "myosin heavy chain" ], "offsets": [ [ 1077, 1095 ] ], "normalized": [] }, { "id": "2376577_T13", "type": "Protein", "text": [ "paramyosin" ], "offsets": [ [ 1097, 1107 ] ], "normalized": [] }, { "id": "2376577_T14", "type": "Protein", "text": [ "alpha-actinin" ], "offsets": [ [ 1127, 1140 ] ], "normalized": [] }, { "id": "2376577_T15", "type": "Protein", "text": [ "elongation factor 1 alpha" ], "offsets": [ [ 1420, 1445 ] ], "normalized": [] }, { "id": "2376577_T16", "type": "Protein", "text": [ "actin" ], "offsets": [ [ 1524, 1529 ] ], "normalized": [] }, { "id": "2376577_T17", "type": "Protein", "text": [ "profilins I" ], "offsets": [ [ 1547, 1558 ] ], "normalized": [] }, { "id": "2376577_T18", "type": "Protein", "text": [ "II" ], "offsets": [ [ 1563, 1565 ] ], "normalized": [] }, { "id": "2376577_T20", "type": "Entity", "text": [ "NH2 terminus" ], "offsets": [ [ 596, 608 ] ], "normalized": [] } ]

[ { "id": "2376577_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 585, 595 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2376577_T8" }, { "role": "Site", "ref_id": "2376577_T20" } ] } ]

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[ { "id": "7068646__text", "type": "abstract", "text": [ "Amino acid sequence and variant forms of favin, a lectin from Vicia faba. \nWe have determined the complete amino acid sequence (182 residues) of the beta chain of favin, the glucose-binding lectin from fava beans (Vicia faba), and have established that the carbohydrate moiety is attached to Asn 168. Together with the sequence of the alpha chain previously reported (Hemperly, J. J., Hopp, T. P., Becker, J. W., and Cunningham, B. A. (1979) J. Biol. Chem. 254, 6803-6810), these data complete the analysis of the primary structure of the lectin. We have also examined minor polypeptides that appear in all preparations of favin. Two lower molecular weight species (Mr = 9,500-11,600) appear to be fragments of the beta chain resulting from cleavage following Asn 76, whereas six high molecular weight forms (Mr = 25,000 or greater) appear to include aggregates of the beta chain and possibly some alternative products of chain processing. " ], "offsets": [ [ 0, 940 ] ] } ]

[ { "id": "7068646_T1", "type": "Protein", "text": [ "favin" ], "offsets": [ [ 41, 46 ] ], "normalized": [] }, { "id": "7068646_T2", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 50, 56 ] ], "normalized": [] }, { "id": "7068646_T3", "type": "Protein", "text": [ "favin" ], "offsets": [ [ 163, 168 ] ], "normalized": [] }, { "id": "7068646_T4", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 190, 196 ] ], "normalized": [] }, { "id": "7068646_T5", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 539, 545 ] ], "normalized": [] }, { "id": "7068646_T6", "type": "Protein", "text": [ "favin" ], "offsets": [ [ 623, 628 ] ], "normalized": [] }, { "id": "7068646_T8", "type": "Entity", "text": [ "Asn 168" ], "offsets": [ [ 292, 299 ] ], "normalized": [] } ]

[ { "id": "7068646_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate moiety is attached" ], "offsets": [ [ 257, 288 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7068646_T3" }, { "role": "Site", "ref_id": "7068646_T8" } ] } ]

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[ { "id": "7836463__text", "type": "abstract", "text": [ "Lumenal orientation and post-translational modifications of the liver microsomal 11 beta-hydroxysteroid dehydrogenase. \nThe topology and post-translational modifications of microsomal 11 beta-hydroxysteroid dehydrogenase (11 beta-DH) was investigated using the approaches of protein structure analysis. Sequence analysis of peptides generated by chemical and enzymatic cleavages revealed that carbohydrate is attached at Asn-122, -161, and -206. Enzymatic deglycosylation reactions of the protein identified the attached glycans as high mannose carbohydrates, implying that the bulk of the protein molecule is oriented on the lumenal side of the endoplasmic membrane. The carbohydrate moiety of native dehydrogenase was cleaved by endo-N-acetylglucosaminidase H without significantly affecting the 11 beta-DH activity. Chemical modification of cysteinyl residues, followed by amino acid sequence analysis, identified one disulfide bond linking Cys-77 and Cys-212. This disulfide bond was inaccessible to thiol reagents, unless the protein was denatured. Contrary to the partially purified 11 beta-DH preparations, the purified enzymatically active protein failed to bind to a 2,5'-ADP affinity column, suggesting that a conformational change has occurred in the enzyme during purification. The proposed model of the 11 beta-DH has a single trans-membrane segment at the N terminus, with the bulk of the polypeptide chain projecting into the lumen of endoplasmic reticulum. Limited proteolysis studies of 11 beta-DH concluded an absence of a flexible intradomain segment between the membranous and the lumenal domains. The lumenal localization of the 11 beta-DH requires a mechanism by which cortisol is transported to the endoplasmic reticulum of the lumen. " ], "offsets": [ [ 0, 1758 ] ] } ]

[ { "id": "7836463_T1", "type": "Protein", "text": [ "11 beta-hydroxysteroid dehydrogenase" ], "offsets": [ [ 81, 117 ] ], "normalized": [] }, { "id": "7836463_T2", "type": "Protein", "text": [ "11 beta-hydroxysteroid dehydrogenase" ], "offsets": [ [ 184, 220 ] ], "normalized": [] }, { "id": "7836463_T3", "type": "Protein", "text": [ "11 beta-DH" ], "offsets": [ [ 222, 232 ] ], "normalized": [] }, { "id": "7836463_T4", "type": "Protein", "text": [ "11 beta-DH" ], "offsets": [ [ 798, 808 ] ], "normalized": [] }, { "id": "7836463_T5", "type": "Protein", "text": [ "11 beta-DH" ], "offsets": [ [ 1089, 1099 ] ], "normalized": [] }, { "id": "7836463_T6", "type": "Protein", "text": [ "11 beta-DH" ], "offsets": [ [ 1316, 1326 ] ], "normalized": [] }, { "id": "7836463_T7", "type": "Protein", "text": [ "11 beta-DH" ], "offsets": [ [ 1504, 1514 ] ], "normalized": [] }, { "id": "7836463_T8", "type": "Protein", "text": [ "11 beta-DH" ], "offsets": [ [ 1650, 1660 ] ], "normalized": [] }, { "id": "7836463_T10", "type": "Entity", "text": [ "Asn-122" ], "offsets": [ [ 421, 428 ] ], "normalized": [] }, { "id": "7836463_T11", "type": "Entity", "text": [ "-161" ], "offsets": [ [ 430, 434 ] ], "normalized": [] }, { "id": "7836463_T12", "type": "Entity", "text": [ "-206" ], "offsets": [ [ 440, 444 ] ], "normalized": [] } ]

[ { "id": "7836463_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate is attached" ], "offsets": [ [ 393, 417 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7836463_T3" }, { "role": "Site", "ref_id": "7836463_T10" } ] }, { "id": "7836463_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate is attached" ], "offsets": [ [ 393, 417 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7836463_T3" }, { "role": "Site", "ref_id": "7836463_T11" } ] }, { "id": "7836463_E3", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate is attached" ], "offsets": [ [ 393, 417 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "7836463_T3" }, { "role": "Site", "ref_id": "7836463_T12" } ] } ]

[ { "id": "7836463_1", "entity_ids": [ "7836463_T3", "7836463_T2" ] } ]

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[ { "id": "3532107__text", "type": "abstract", "text": [ "Structural evidence that endothelial cell growth factor beta is the precursor of both endothelial cell growth factor alpha and acidic fibroblast growth factor. \nTwo endothelial cell growth factors (ECGF) have been purified from bovine brain and termed alpha- and beta-ECGF [Burgess, W. H., Mehlman, T., Friesel, R., Johnson, W. V. & Maciag, T. (1985) J. Biol. Chem. 260, 11389-11392]. Amino acid sequence analysis indicates that beta-ECGF represents a 20 amino acid amino-terminal extension of alpha-ECGF and a 14 amino acid amino-terminal extension of acidic fibroblast growth factor. These data indicate that both alpha-ECGF and acidic fibroblast growth factor may be derived from beta-ECGF by posttranslational processing. Analysis of the amino-terminal 14 residues of beta-ECGF by fast-atom-bombardment mass spectrometry established the amino acid sequence of this region and the identity of the blocking group at the amino terminus (acetyl). " ], "offsets": [ [ 0, 947 ] ] } ]

[ { "id": "3532107_T1", "type": "Protein", "text": [ "endothelial cell growth factor beta" ], "offsets": [ [ 25, 60 ] ], "normalized": [] }, { "id": "3532107_T2", "type": "Protein", "text": [ "endothelial cell growth factor alpha" ], "offsets": [ [ 86, 122 ] ], "normalized": [] }, { "id": "3532107_T3", "type": "Protein", "text": [ "acidic fibroblast growth factor" ], "offsets": [ [ 127, 158 ] ], "normalized": [] }, { "id": "3532107_T4", "type": "Protein", "text": [ "alpha-" ], "offsets": [ [ 252, 258 ] ], "normalized": [] }, { "id": "3532107_T5", "type": "Protein", "text": [ "beta-ECGF" ], "offsets": [ [ 263, 272 ] ], "normalized": [] }, { "id": "3532107_T6", "type": "Protein", "text": [ "beta-ECGF" ], "offsets": [ [ 429, 438 ] ], "normalized": [] }, { "id": "3532107_T7", "type": "Protein", "text": [ "alpha-ECGF" ], "offsets": [ [ 494, 504 ] ], "normalized": [] }, { "id": "3532107_T8", "type": "Protein", "text": [ "acidic fibroblast growth factor" ], "offsets": [ [ 553, 584 ] ], "normalized": [] }, { "id": "3532107_T9", "type": "Protein", "text": [ "alpha-ECGF" ], "offsets": [ [ 616, 626 ] ], "normalized": [] }, { "id": "3532107_T10", "type": "Protein", "text": [ "acidic fibroblast growth factor" ], "offsets": [ [ 631, 662 ] ], "normalized": [] }, { "id": "3532107_T11", "type": "Protein", "text": [ "beta-ECGF" ], "offsets": [ [ 683, 692 ] ], "normalized": [] }, { "id": "3532107_T12", "type": "Protein", "text": [ "beta-ECGF" ], "offsets": [ [ 772, 781 ] ], "normalized": [] }, { "id": "3532107_T13", "type": "Entity", "text": [ "amino-terminal 14 residues" ], "offsets": [ [ 742, 768 ] ], "normalized": [] } ]

[ { "id": "3532107_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "blocking group at the amino terminus (acetyl)" ], "offsets": [ [ 900, 945 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3532107_T12" }, { "role": "Site", "ref_id": "3532107_T13" } ] } ]

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[ { "id": "1148223__text", "type": "abstract", "text": [ "The effect of vitamin D on the structural crosslinks and maturation of chick bone collagen. \nThe quantitative relationships were determined between the structural crosslinks, dihydroxylysinonorleucine (Lys(OH)2-Nle) and hydroxylysinonorleucine (Lys (OH) -Nle) in NaB 3H4-reduced diaphyseal bone collagen from 1-, 2-, 3- and 4-week-old chicks fed either a vitamin D-deficient diet, a normal-vitamin D diet or a high-, but non toxic, vitamin D diet from time of hatching. Chicks fed the normal diet showed a progressive decrease in the ratio of Lys(OH)2-Nle/Lys(OH)-Nle with age. This decrease was accelerated in chicks receiving the High-vitamin D diet. In the vitamin D-deficient group, the ratio was higher than controls at 1 and 2 weeks and increased further at 3 and 4 weeks. Similar changes in Lys(OH)2-Nle/Lys(OH)-Nle ratio did not occur in skin collagen. Compared to Control-vitamin D animals, the increased crosslink ratios in the vitamin D-deficient bone collagen occurred prior to changes in growth rate and could not be correlated with lysine hydroxylation or the hypocalcemia seen in this group. These results suggest that the type of crosslink analysis used in this study provides one of the earliest and most sensitive indications of a bone disturbance due to vitamin D deficiency and that vitamin D specifically acts to increase the rate of maturation of bone collagen. " ], "offsets": [ [ 0, 1384 ] ] } ]

[ { "id": "1148223_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 82, 90 ] ], "normalized": [] }, { "id": "1148223_T2", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 295, 303 ] ], "normalized": [] }, { "id": "1148223_T3", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 851, 859 ] ], "normalized": [] }, { "id": "1148223_T4", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 963, 971 ] ], "normalized": [] }, { "id": "1148223_T5", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 1374, 1382 ] ], "normalized": [] }, { "id": "1148223_T6", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 1046, 1052 ] ], "normalized": [] } ]

[ { "id": "1148223_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1053, 1066 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1148223_T4" }, { "role": "Site", "ref_id": "1148223_T6" } ] } ]

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[ { "id": "12410229__text", "type": "abstract", "text": [ "Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. \nGenes located in chromosomal regions near telomeres are transcriptionally silent, whereas those located in regions away from telomeres are not. Here we show that there is a gradient of acetylation of histone H4 at lysine 16 (H4-Lys16) along a yeast chromosome; this gradient ranges from a hypoacetylated state in regions near the telomere to a hyperacetylated state in more distant regions. The hyperacetylation is regulated by Sas2p, a member of the MYST-type family of histone acetylases, whereas hypoacetylation is under the control of Sir2p, a histone deacetylase. Loss of hyperacetylation is accompanied by an increase in localization of the telomere protein Sir3p and the inactivation of gene expression in telomere-distal regions. Thus, the Sas2p and Sir2p function in concert to regulate transcription in yeast, by acetylating and deacetylating H4-Lys16 in a mechanism that may be common to all eukaryotes. " ], "offsets": [ [ 0, 1037 ] ] } ]

[ { "id": "12410229_T1", "type": "Protein", "text": [ "Sas2p" ], "offsets": [ [ 59, 64 ] ], "normalized": [] }, { "id": "12410229_T2", "type": "Protein", "text": [ "Sir2p" ], "offsets": [ [ 69, 74 ] ], "normalized": [] }, { "id": "12410229_T3", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 330, 332 ] ], "normalized": [] }, { "id": "12410229_T4", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 347, 349 ] ], "normalized": [] }, { "id": "12410229_T5", "type": "Protein", "text": [ "Sas2p" ], "offsets": [ [ 550, 555 ] ], "normalized": [] }, { "id": "12410229_T6", "type": "Protein", "text": [ "Sir2p" ], "offsets": [ [ 661, 666 ] ], "normalized": [] }, { "id": "12410229_T7", "type": "Protein", "text": [ "Sir3p" ], "offsets": [ [ 786, 791 ] ], "normalized": [] }, { "id": "12410229_T8", "type": "Protein", "text": [ "Sas2p" ], "offsets": [ [ 870, 875 ] ], "normalized": [] }, { "id": "12410229_T9", "type": "Protein", "text": [ "Sir2p" ], "offsets": [ [ 880, 885 ] ], "normalized": [] }, { "id": "12410229_T10", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 975, 977 ] ], "normalized": [] }, { "id": "12410229_T12", "type": "Entity", "text": [ "lysine 16" ], "offsets": [ [ 336, 345 ] ], "normalized": [] }, { "id": "12410229_T14", "type": "Entity", "text": [ "Lys16" ], "offsets": [ [ 978, 983 ] ], "normalized": [] } ]

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[ { "id": "12410229_1", "entity_ids": [ "12410229_T3", "12410229_T4" ] } ]

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[ { "id": "1990011__text", "type": "abstract", "text": [ "Bovine glomerular basement membrane. Location and structure of the asparagine-linked oligosaccharide units and their potential role in the assembly of the 7 S collagen IV tetramer. \nCollagen IV contains an amino-terminal tetramerization domain (7 S) that is involved in aggregation and cross-linking as part of the process of self-assembly of the collagen IV matrix of basement membranes. We determined the structure and location of the Asn-linked oligosaccharides of the 7 S tetramer. Two glycopeptides, GP-1 and GP-2, were isolated from tryptic digests of the 7 S tetramer and were characterized. GP-1 and GP-2 are derived from the alpha 1(IV) chain and the alpha 2(IV) chain, respectively. Each glycopeptide contained one sequence, -Asn-Xaa-Thr-, which was shown to be N-glycosylated at Asn, corresponding to position 126 of the alpha 1 chains and 138 of the alpha 2 chain. 1H NMR spectroscopic analysis of the oligosaccharide is a biantennary N-acetyllactosamine type of N-linked oligosaccharide with a broad heterogeneity in the presence of the sugar residues at their nonreducing termini as indicated. [formula: see text] The location of the Asn-linked oligosaccharide units and Hyl-linked disaccharide units and their orientation with respect to the surface of the triple helix were calculated using two models. We conclude that both units are important determinants in the assembly of the 7 S tetramer. " ], "offsets": [ [ 0, 1411 ] ] } ]

[ { "id": "1990011_T1", "type": "Protein", "text": [ "collagen IV" ], "offsets": [ [ 159, 170 ] ], "normalized": [] }, { "id": "1990011_T2", "type": "Protein", "text": [ "Collagen IV" ], "offsets": [ [ 182, 193 ] ], "normalized": [] }, { "id": "1990011_T3", "type": "Protein", "text": [ "collagen IV" ], "offsets": [ [ 347, 358 ] ], "normalized": [] }, { "id": "1990011_T4", "type": "Protein", "text": [ "alpha 1(IV) chain" ], "offsets": [ [ 634, 651 ] ], "normalized": [] }, { "id": "1990011_T5", "type": "Protein", "text": [ "alpha 2(IV) chain" ], "offsets": [ [ 660, 677 ] ], "normalized": [] }, { "id": "1990011_T7", "type": "Entity", "text": [ "Asn" ], "offsets": [ [ 790, 793 ] ], "normalized": [] } ]

[ { "id": "1990011_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "N-glycosylated" ], "offsets": [ [ 772, 786 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1990011_T4" }, { "role": "Site", "ref_id": "1990011_T7" } ] }, { "id": "1990011_E2", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "N-glycosylated" ], "offsets": [ [ 772, 786 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1990011_T5" }, { "role": "Site", "ref_id": "1990011_T7" } ] } ]

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[ { "id": "1402806__text", "type": "abstract", "text": [ "Sequence analysis of the membrane protein gene of human coronavirus OC43 and evidence for O-glycosylation. \nThe gene encoding the membrane (M) protein of the OC43 strain of human coronavirus (HCV-OC43) was amplified by a reverse transcription-polymerase chain reaction of viral RNA with HCV-OC43- and bovine coronavirus (BCV)-specific primers. The nucleotide sequence of the cloned 1.5 kb fragment revealed an open reading frame (ORF) of 690 nucleotides which was identified as the M protein gene from its homology to BCV. This ORF encodes a protein of 230 amino acids with an M(r) of 26416. The gene is preceded by the motif UCCAAAC, analogous to the consensus coronavirus transcription initiation sequence. The M protein of HCV-OC43 shows features typical of all coronavirus M proteins studied: a hydrophilic, presumably external N terminus including about 10% of the protein, and a potential N-glycosylation site followed by three major hydrophobic transmembrane domains. The amino acid sequence of the M protein of HCV-OC43 has 94% identity with that of the Mebus strain of BCV, and also contains six potential O-glycosylation sites in the exposed N-terminal domain. Indeed, the glycosylation of the M protein was not inhibited in the presence of tunicamycin, which is indicative of O-glycosylation, as previously reported for BCV and murine hepatitis virus. Virions released from tunicamycin-treated cells contained the M glycoprotein but were devoid of both peplomer (S) and haemagglutinin-esterase (HE) proteins. Thus, inhibition of the N-glycosylation of the S and HE structural proteins prevented their incorporation into progeny virions, an indication that they are dispensable for virion morphogenesis, unlike the M protein. " ], "offsets": [ [ 0, 1736 ] ] } ]

[ { "id": "1402806_T1", "type": "Protein", "text": [ "M protein" ], "offsets": [ [ 1006, 1015 ] ], "normalized": [] }, { "id": "1402806_T3", "type": "Entity", "text": [ "N-terminal domain" ], "offsets": [ [ 1152, 1169 ] ], "normalized": [] } ]

[ { "id": "1402806_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "potential O-glycosylation sites" ], "offsets": [ [ 1105, 1136 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1402806_T1" }, { "role": "Site", "ref_id": "1402806_T3" } ] } ]

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[ { "id": "18408754__text", "type": "abstract", "text": [ "Histone H4 lysine 20 monomethylation promotes transcriptional repression by L3MBTL1. \nLethal 3 malignant brain tumor 1 (L3MBTL1), a homolog of the Drosophila polycomb tumor suppressor l(3)mbt, contains three tandem MBT repeats (3xMBT) that are critical for transcriptional repression. We recently reported that the 3xMBT repeats interact with mono- and dimethylated lysines in the amino termini of histones H4 and H1b to promote methylation-dependent chromatin compaction. Using a series of histone peptides, we now show that the recognition of mono- and dimethylated lysines in histones H3, H4 and H1.4 (but not their trimethylated or unmodified counterparts) by 3xMBT occurs in the context of a basic environment, requiring a conserved aspartic acid (D355) in the second MBT repeat. Despite the broad range of in vitro binding, the chromatin association of L3MBTL1 mirrors the progressive accumulation of H4K20 monomethylation during the cell cycle. Furthermore, transcriptional repression by L3MBTL1 is enhanced by the H4K20 monomethyltransferase PR-SET7 (to which it binds) but not SUV420H1 (an H4K20 trimethylase) or G9a (an H3K9 dimethylase) and knockdown of PR-SET7 decreases H4K20me1 levels and the chromatin association of L3MBTL1. Our studies identify the importance of H4K20 monomethylation and of PR-SET7 for L3MBTL1 function. " ], "offsets": [ [ 0, 1339 ] ] } ]

[ { "id": "18408754_T1", "type": "Protein", "text": [ "Histone H4" ], "offsets": [ [ 0, 10 ] ], "normalized": [] }, { "id": "18408754_T2", "type": "Protein", "text": [ "histones H4" ], "offsets": [ [ 398, 409 ] ], "normalized": [] }, { "id": "18408754_T3", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 414, 417 ] ], "normalized": [] }, { "id": "18408754_T4", "type": "Protein", "text": [ "histones H3" ], "offsets": [ [ 579, 590 ] ], "normalized": [] }, { "id": "18408754_T5", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 592, 594 ] ], "normalized": [] }, { "id": "18408754_T6", "type": "Protein", "text": [ "H1.4" ], "offsets": [ [ 599, 603 ] ], "normalized": [] }, { "id": "18408754_T7", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 907, 909 ] ], "normalized": [] }, { "id": "18408754_T8", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1022, 1024 ] ], "normalized": [] }, { "id": "18408754_T9", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1099, 1101 ] ], "normalized": [] }, { "id": "18408754_T10", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 1130, 1132 ] ], "normalized": [] }, { "id": "18408754_T11", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1183, 1185 ] ], "normalized": [] }, { "id": "18408754_T12", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1280, 1282 ] ], "normalized": [] }, { "id": "18408754_T13", "type": "Entity", "text": [ "lysine 20" ], "offsets": [ [ 11, 20 ] ], "normalized": [] }, { "id": "18408754_T17", "type": "Entity", "text": [ "lysines" ], "offsets": [ [ 366, 373 ] ], "normalized": [] }, { "id": "18408754_T20", "type": "Entity", "text": [ "lysines" ], "offsets": [ [ 568, 575 ] ], "normalized": [] }, { "id": "18408754_T21", "type": "Entity", "text": [ "K20" ], "offsets": [ [ 909, 912 ] ], "normalized": [] }, { "id": "18408754_T23", "type": "Entity", "text": [ "K20" ], "offsets": [ [ 1282, 1285 ] ], "normalized": [] } ]

[ { "id": "18408754_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "monomethylation" ], "offsets": [ [ 21, 36 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T1" }, { "role": "Site", "ref_id": "18408754_T13" } ] }, { "id": "18408754_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "mono-" ], "offsets": [ [ 343, 348 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T2" }, { "role": "Site", "ref_id": "18408754_T17" } ] }, { "id": "18408754_E3", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "mono-" ], "offsets": [ [ 343, 348 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T3" }, { "role": "Site", "ref_id": "18408754_T17" } ] }, { "id": "18408754_E4", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "dimethylated" ], "offsets": [ [ 353, 365 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T3" }, { "role": "Site", "ref_id": "18408754_T17" } ] }, { "id": "18408754_E5", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "dimethylated" ], "offsets": [ [ 353, 365 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T2" }, { "role": "Site", "ref_id": "18408754_T17" } ] }, { "id": "18408754_E6", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "mono-" ], "offsets": [ [ 545, 550 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T4" }, { "role": "Site", "ref_id": "18408754_T20" } ] }, { "id": "18408754_E7", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "mono-" ], "offsets": [ [ 545, 550 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T6" }, { "role": "Site", "ref_id": "18408754_T20" } ] }, { "id": "18408754_E8", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "mono-" ], "offsets": [ [ 545, 550 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T5" }, { "role": "Site", "ref_id": "18408754_T20" } ] }, { "id": "18408754_E9", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "dimethylated" ], "offsets": [ [ 555, 567 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T4" }, { "role": "Site", "ref_id": "18408754_T20" } ] }, { "id": "18408754_E10", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "dimethylated" ], "offsets": [ [ 555, 567 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T5" }, { "role": "Site", "ref_id": "18408754_T20" } ] }, { "id": "18408754_E11", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "dimethylated" ], "offsets": [ [ 555, 567 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T6" }, { "role": "Site", "ref_id": "18408754_T20" } ] }, { "id": "18408754_E12", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "monomethylation" ], "offsets": [ [ 913, 928 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T7" }, { "role": "Site", "ref_id": "18408754_T21" } ] }, { "id": "18408754_E13", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "monomethylation" ], "offsets": [ [ 1286, 1301 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "18408754_T12" }, { "role": "Site", "ref_id": "18408754_T23" } ] } ]

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[ { "id": "5167020__text", "type": "abstract", "text": [ "Amino acid sequence and sequence variability of the amino-terminal regions of lysine-rich histones. \nThe amino acid sequence has been determined for the first 72 residues of a lysine-rich histone from rabbit thymus. These are the residues contained in a fragment released from the histone by treatment with N-bromosuccinimide. Peptides derived by tryptic, thermolysin, and chymotryptic digestion of this 72-residue fragment were used to reconstruct the total sequence. Analysis of the sequence revealed some unusual aspects of the structure of the fragment, which comprises about one-third of the histone molecule. Thirty of the first 40 residues are accounted for by lysine, alanine, and proline; this portion of the fragment includes sequences of 4,2, and 3 consecutive basic residues. The last 32 residues contain all the hydrophobic amino acids (valine, isoleucine, leucine, tyrosine) of the fragment but have few basic residues and no prolines. The NH2 terminus of the histone is acetylated. Comparison of the sequence of the NH2-terminal half of this lysine-rich histone with the entire sequences of the slightly lysine-rich and arginine-rich histones shows that all three have similar characteristics, that is, an NH2-terminal region rich in basic amino acids and a COOH-terminal portion rich in hydrophobic residues. Tryptic peptides from the NH2-terminal N-bromosuccinimide fragment of two other thymus lysine-rich histones have been isolated. These peptides (with partial sequences) were aligned by direct identity or analogy with the complete amino acid sequence of the NH2-terminal N-bromosuccinimide fragment of the lysine-rich histone studied previously. It was found that there were from 7 to 14 amino acid differences between fractions. One of the amino acid interchanges eliminates a major phosphorylation site. " ], "offsets": [ [ 0, 1829 ] ] } ]

[ { "id": "5167020_T1", "type": "Protein", "text": [ "lysine-rich histones" ], "offsets": [ [ 78, 98 ] ], "normalized": [] }, { "id": "5167020_T2", "type": "Protein", "text": [ "lysine-rich histone" ], "offsets": [ [ 176, 195 ] ], "normalized": [] }, { "id": "5167020_T3", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 597, 604 ] ], "normalized": [] }, { "id": "5167020_T4", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 974, 981 ] ], "normalized": [] }, { "id": "5167020_T5", "type": "Protein", "text": [ "lysine-rich histone" ], "offsets": [ [ 1057, 1076 ] ], "normalized": [] }, { "id": "5167020_T6", "type": "Protein", "text": [ "lysine-rich" ], "offsets": [ [ 1119, 1130 ] ], "normalized": [] }, { "id": "5167020_T7", "type": "Protein", "text": [ "arginine-rich histones" ], "offsets": [ [ 1135, 1157 ] ], "normalized": [] }, { "id": "5167020_T8", "type": "Protein", "text": [ "lysine-rich histones" ], "offsets": [ [ 1412, 1432 ] ], "normalized": [] }, { "id": "5167020_T9", "type": "Protein", "text": [ "lysine-rich histon" ], "offsets": [ [ 1629, 1647 ] ], "normalized": [] }, { "id": "5167020_T10", "type": "Entity", "text": [ "NH2 terminus" ], "offsets": [ [ 954, 966 ] ], "normalized": [] } ]

[ { "id": "5167020_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 985, 995 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "5167020_T4" }, { "role": "Site", "ref_id": "5167020_T10" } ] } ]

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[ { "id": "3698056__text", "type": "abstract", "text": [ "Structures of the carbohydrate moiety attached to one site in the first domain of turkey ovomucoid: elucidation by 1H-n.m.r. spectroscopy. \n1H-N.m.r. spectroscopy was used to elucidate the primary structures of the carbohydrate moiety attached to asparagine at residue 53 in the first domain of turkey ovomucoid, a serine proteinase inhibitor. The carbohydrate moiety is a heterogeneous mixture of three structurally closely related complex-type oligosaccharides. Of the total carbohydrate moiety, 61% is tetra-antennary with terminal galactose and with an intersecting N-acetylglucosamine, and containing an additional N-acetylglucosamine (10') attached to mannose (4'). Another 23% is tri-antennary with terminal galactose and with an intersecting N-acetylglucosamine. The remaining 16% is tri-antennary with terminal galactose (6 and 8 only), with an intersecting N-acetylglucosamine. " ], "offsets": [ [ 0, 888 ] ] } ]

[ { "id": "3698056_T1", "type": "Protein", "text": [ "ovomucoid" ], "offsets": [ [ 89, 98 ] ], "normalized": [] }, { "id": "3698056_T2", "type": "Protein", "text": [ "ovomucoid" ], "offsets": [ [ 302, 311 ] ], "normalized": [] }, { "id": "3698056_T4", "type": "Entity", "text": [ "asparagine" ], "offsets": [ [ 247, 257 ] ], "normalized": [] } ]

[ { "id": "3698056_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "carbohydrate moiety attached" ], "offsets": [ [ 215, 243 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3698056_T2" }, { "role": "Site", "ref_id": "3698056_T4" } ] } ]

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[ { "id": "2752049__text", "type": "abstract", "text": [ "Structure of cytochrome b5 and its topology in the microsomal membrane. \nThe complete amino acid sequence of human and chicken liver microsomal cytochrome b5 was determined. The amino termini of cytochrome b5 from four other mammalian species were examined in order to determine their complete covalent structure. As in the rat species, cytochrome b5 preparations from man, rabbit, calf and horse had an acetylated alanine as the first residue. In contrast, the pig cytochrome had alanine at the amino terminus. The amino terminus of the chicken cytochrome b5 was also unmodified, and extended three residues absent in the mammalian species. In order to investigate whether the carboxy-terminal segment of cytochrome b5 is located on the cytosolic or the luminal side of the microsomal membrane, rabbit liver microsomes were treated with trypsin and subjected to gel filtration and high-pressure liquid chromatography. The nonpolar peptide isolated from these microsomes lacked the terminal hexapeptide, indicating that when cytochrome b5 is bound to intact microsomes, the carboxy terminus is located on the cytosolic side of the membrane and does not extend in the lumen of the endoplasmic reticulum. " ], "offsets": [ [ 0, 1203 ] ] } ]

[ { "id": "2752049_T1", "type": "Protein", "text": [ "cytochrome b5" ], "offsets": [ [ 13, 26 ] ], "normalized": [] }, { "id": "2752049_T2", "type": "Protein", "text": [ "cytochrome b5" ], "offsets": [ [ 144, 157 ] ], "normalized": [] }, { "id": "2752049_T3", "type": "Protein", "text": [ "cytochrome b5" ], "offsets": [ [ 195, 208 ] ], "normalized": [] }, { "id": "2752049_T4", "type": "Protein", "text": [ "cytochrome b5" ], "offsets": [ [ 337, 350 ] ], "normalized": [] }, { "id": "2752049_T5", "type": "Protein", "text": [ "cytochrome b5" ], "offsets": [ [ 546, 559 ] ], "normalized": [] }, { "id": "2752049_T6", "type": "Protein", "text": [ "cytochrome b5" ], "offsets": [ [ 706, 719 ] ], "normalized": [] }, { "id": "2752049_T7", "type": "Protein", "text": [ "cytochrome b5" ], "offsets": [ [ 1025, 1038 ] ], "normalized": [] }, { "id": "2752049_T9", "type": "Entity", "text": [ "alanine" ], "offsets": [ [ 415, 422 ] ], "normalized": [] } ]

[ { "id": "2752049_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 404, 414 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "2752049_T4" }, { "role": "Site", "ref_id": "2752049_T9" } ] } ]

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[ { "id": "3264725__text", "type": "abstract", "text": [ "Amino acid sequence and posttranslational modifications of human factor VIIa from plasma and transfected baby hamster kidney cells. \nBlood coagulation factor VII is a vitamin K dependent glycoprotein which in its activated form, factor VIIa, participates in the coagulation process by activating factor X and/or factor IX in the presence of Ca2+ and tissue factor. Three types of potential posttranslational modifications exist in the human factor VIIa molecule, namely, 10 gamma-carboxylated, N-terminally located glutamic acid residues, 1 beta-hydroxylated aspartic acid residue, and 2 N-glycosylated asparagine residues. In the present study, the amino acid sequence and posttranslational modifications of recombinant factor VIIa as purified from the culture medium of a transfected baby hamster kidney cell line have been compared to human plasma factor VIIa. By use of HPLC, amino acid analysis, peptide mapping, and automated Edman degradations, the protein backbone of recombinant factor VIIa was found to be identical with human factor VIIa. Neither recombinant factor VIIa nor human plasma factor VIIa was found to contain beta-hydroxyaspartic acid. In human plasma factor VIIa, the 10 N-terminally located glutamic acid residues were found to be fully gamma-carboxylated whereas 9 full and 1 partial gamma-carboxylated residues were found in the corresponding positions of the recombinant factor VIIa molecule. Asparagine residues 145 and 322 were found to be fully N-glycosylated in human plasma factor VIIa. In the recombinant factor VIIa, asparagine residue 322 was fully glycosylated whereas asparagine residue 145 was only partially (approximately 66%) glycosylated. Besides minor differences in the sialic acid and fucose contents, the overall carbohydrate compositions were nearly identical in recombinant factor VIIa and human plasma factor VIIa. (ABSTRACT TRUNCATED AT 250 WORDS) " ], "offsets": [ [ 0, 1899 ] ] } ]

[ { "id": "3264725_T1", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 65, 76 ] ], "normalized": [] }, { "id": "3264725_T2", "type": "Protein", "text": [ "coagulation factor VII" ], "offsets": [ [ 139, 161 ] ], "normalized": [] }, { "id": "3264725_T3", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 229, 240 ] ], "normalized": [] }, { "id": "3264725_T4", "type": "Protein", "text": [ "factor X" ], "offsets": [ [ 296, 304 ] ], "normalized": [] }, { "id": "3264725_T5", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 312, 321 ] ], "normalized": [] }, { "id": "3264725_T6", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 441, 452 ] ], "normalized": [] }, { "id": "3264725_T7", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 721, 732 ] ], "normalized": [] }, { "id": "3264725_T8", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 851, 862 ] ], "normalized": [] }, { "id": "3264725_T9", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 988, 999 ] ], "normalized": [] }, { "id": "3264725_T10", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1037, 1048 ] ], "normalized": [] }, { "id": "3264725_T11", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1070, 1081 ] ], "normalized": [] }, { "id": "3264725_T12", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1099, 1110 ] ], "normalized": [] }, { "id": "3264725_T13", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1175, 1186 ] ], "normalized": [] }, { "id": "3264725_T14", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1399, 1410 ] ], "normalized": [] }, { "id": "3264725_T15", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1507, 1518 ] ], "normalized": [] }, { "id": "3264725_T16", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1539, 1550 ] ], "normalized": [] }, { "id": "3264725_T17", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1823, 1834 ] ], "normalized": [] }, { "id": "3264725_T18", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1852, 1863 ] ], "normalized": [] }, { "id": "3264725_T20", "type": "Entity", "text": [ "glutamic acid" ], "offsets": [ [ 515, 528 ] ], "normalized": [] }, { "id": "3264725_T22", "type": "Entity", "text": [ "aspartic acid" ], "offsets": [ [ 559, 572 ] ], "normalized": [] }, { "id": "3264725_T24", "type": "Entity", "text": [ "asparagine" ], "offsets": [ [ 603, 613 ] ], "normalized": [] }, { "id": "3264725_T25", "type": "Entity", "text": [ "glutamic acid" ], "offsets": [ [ 1216, 1229 ] ], "normalized": [] }, { "id": "3264725_T27", "type": "Entity", "text": [ "Asparagine residues 145" ], "offsets": [ [ 1421, 1444 ] ], "normalized": [] }, { "id": "3264725_T28", "type": "Entity", "text": [ "322" ], "offsets": [ [ 1449, 1452 ] ], "normalized": [] } ]

[ { "id": "3264725_E1", "type": "Protein_modification", "trigger": { "text": [ "carboxylated" ], "offsets": [ [ 480, 492 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3264725_T6" }, { "role": "Site", "ref_id": "3264725_T20" } ] }, { "id": "3264725_E2", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 546, 558 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3264725_T6" }, { "role": "Site", "ref_id": "3264725_T22" } ] }, { "id": "3264725_E3", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 590, 602 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3264725_T6" }, { "role": "Site", "ref_id": "3264725_T24" } ] }, { "id": "3264725_E4", "type": "Protein_modification", "trigger": { "text": [ "gamma-carboxylated" ], "offsets": [ [ 1262, 1280 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3264725_T13" }, { "role": "Site", "ref_id": "3264725_T25" } ] }, { "id": "3264725_E5", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "N-glycosylated" ], "offsets": [ [ 1476, 1490 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3264725_T15" }, { "role": "Site", "ref_id": "3264725_T28" } ] }, { "id": "3264725_E6", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "N-glycosylated" ], "offsets": [ [ 1476, 1490 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "3264725_T15" }, { "role": "Site", "ref_id": "3264725_T27" } ] } ]

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[ { "id": "5144717__text", "type": "abstract", "text": [ "Studies on the hydroxylation of lysine occurring in the non-helical region at the N-terminal end of the collagen molecule. \n" ], "offsets": [ [ 0, 124 ] ] } ]

[ { "id": "5144717_T1", "type": "Protein", "text": [ "collagen" ], "offsets": [ [ 104, 112 ] ], "normalized": [] }, { "id": "5144717_T3", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 32, 38 ] ], "normalized": [] } ]

[ { "id": "5144717_E1", "type": "Protein_amino_acid_hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 15, 28 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "5144717_T1" }, { "role": "Site", "ref_id": "5144717_T3" } ] } ]

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[ { "id": "6406481__text", "type": "abstract", "text": [ "Amino acid sequence of porcine spleen cathepsin D light chain. \nThe complete amino acid sequence of the light chain of cathepsin D from porcine spleen has been determined. The light chain consists of a single polypeptide chain with 97 amino acid residues. The sequence is: (formula; see text) The molecular weight of the light chain was calculated from this sequence to be 10,548 (without carbohydrates). A single disulfide bond links two half-cystine residues between positions 46 and 53. A cysteine residue is located at position 27. The light chain sequence is extensively homologous to the NH2-terminal sequence of other aspartyl proteases. It shows a 59% identity with the sequence of mouse submaxillary gland renin and a 49% identity with that of porcine pepsin. A single glycosylation site is located at residue 70 of the cathepsin D light chain. This site corresponds to position 67 of pepsin by homology. The active site aspartyl residue, corresponding to Asp-32 of pepsin, is located at residue 33 in the cathepsin D light chain. " ], "offsets": [ [ 0, 1040 ] ] } ]

[ { "id": "6406481_T1", "type": "Protein", "text": [ "cathepsin D light chain" ], "offsets": [ [ 38, 61 ] ], "normalized": [] }, { "id": "6406481_T2", "type": "Protein", "text": [ "cathepsin D" ], "offsets": [ [ 119, 130 ] ], "normalized": [] }, { "id": "6406481_T3", "type": "Protein", "text": [ "cathepsin D light chain" ], "offsets": [ [ 829, 852 ] ], "normalized": [] }, { "id": "6406481_T4", "type": "Protein", "text": [ "cathepsin D light chain" ], "offsets": [ [ 1015, 1038 ] ], "normalized": [] }, { "id": "6406481_T6", "type": "Entity", "text": [ "residue 70" ], "offsets": [ [ 811, 821 ] ], "normalized": [] } ]

[ { "id": "6406481_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "glycosylation site is located" ], "offsets": [ [ 778, 807 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "6406481_T3" }, { "role": "Site", "ref_id": "6406481_T6" } ] } ]

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[ { "id": "624283__text", "type": "abstract", "text": [ "The amino-acid sequence of chicken fast-skeletal-muscle troponin I. \nThe amino acid sequence of troponin I from chicken breast and leg muscle has been determined using tryptic and CNBr peptides. The protein contains 182 residues and has a molecular weight of 21136. The N-terminus is blocked and is probably acetylated. 35 of the residues have acidic and 45 have basic side chains giving an overall net positive charge of 9. The CNBr peptides from both breast and leg troponin I have been shown to be identical and no heterogeneity has been found in the tryptic peptides isolated from a mixture of the two proteins. It may thus be taken that the two proteins are identical. Comparison with the sequence of troponin I from rabbit fast skeletal muscle shows strong homology with 34 differences out of 182 residues. The major difference is in a deletion of three residues, from 152 to 154, in the rabbit protein. " ], "offsets": [ [ 0, 910 ] ] } ]

[ { "id": "624283_T1", "type": "Protein", "text": [ "troponin I" ], "offsets": [ [ 56, 66 ] ], "normalized": [] }, { "id": "624283_T2", "type": "Protein", "text": [ "troponin I" ], "offsets": [ [ 96, 106 ] ], "normalized": [] }, { "id": "624283_T3", "type": "Protein", "text": [ "troponin I" ], "offsets": [ [ 468, 478 ] ], "normalized": [] }, { "id": "624283_T4", "type": "Protein", "text": [ "troponin I" ], "offsets": [ [ 706, 716 ] ], "normalized": [] }, { "id": "624283_T5", "type": "Entity", "text": [ "N-terminus" ], "offsets": [ [ 270, 280 ] ], "normalized": [] } ]

[ { "id": "624283_E1", "type": "Protein_amino_acid_acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 308, 318 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "624283_T2" }, { "role": "Site", "ref_id": "624283_T5" } ] } ]

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[ { "id": "385603__text", "type": "abstract", "text": [ "In vivo methylation of prokaryotic elongation factor Tu. \nIn Salmonella typhimurium and Escherichia coli, elongation factor Tu (EF-Tu) is methylated as shown by its incorporation of labeled methyl residues from [methyl-3H]methionine. Analysis of the nature of the methyl-containing residues by protein hydrolysis, followed by paper chromatography and high voltage electrophoresis showed that both mono- and dimethyllysine are present. Eighty per cent of the EF-Tu molecules are methylated if methylation occurs at a unique lysine residue. The EF-Tu fraction which is not methylated is still able to accept methyl groups, as shown by methylation of approximately 10% of the EF-Tu after addition of chloramphenicol (D-(-)-threo-2,2-dichloro-N-[beta-hydroxy-alpha-(hydroxymethyl)-o-nitrophenethyl] acetamide) to inhibit further protein synthesis. There is no evidence of turnover of the methyl residues. We attempted to separate the methylated from the nonmethylated form of EF-Tu by isoelectric focusing on polyacrylamide gel, but were unable to do so. " ], "offsets": [ [ 0, 1051 ] ] } ]

[ { "id": "385603_T1", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 35, 55 ] ], "normalized": [] }, { "id": "385603_T2", "type": "Protein", "text": [ "elongation factor Tu" ], "offsets": [ [ 106, 126 ] ], "normalized": [] }, { "id": "385603_T3", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 128, 133 ] ], "normalized": [] }, { "id": "385603_T4", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 458, 463 ] ], "normalized": [] }, { "id": "385603_T5", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 543, 548 ] ], "normalized": [] }, { "id": "385603_T6", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 673, 678 ] ], "normalized": [] }, { "id": "385603_T7", "type": "Protein", "text": [ "EF-Tu" ], "offsets": [ [ 972, 977 ] ], "normalized": [] }, { "id": "385603_T10", "type": "Entity", "text": [ "[methyl-3H]methionine" ], "offsets": [ [ 211, 232 ] ], "normalized": [] }, { "id": "385603_T12", "type": "Entity", "text": [ "lysine residue" ], "offsets": [ [ 523, 537 ] ], "normalized": [] } ]

[ { "id": "385603_E1", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 8, 19 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "385603_T1" } ] }, { "id": "385603_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 138, 148 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "385603_T3" }, { "role": "Site", "ref_id": "385603_T10" } ] }, { "id": "385603_E3", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 478, 488 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "385603_T4" }, { "role": "Site", "ref_id": "385603_T12" } ] }, { "id": "385603_E4", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 571, 581 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "385603_T5" } ] }, { "id": "385603_E5", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 633, 644 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "385603_T6" } ] }, { "id": "385603_E6", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 930, 940 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "385603_T7" } ] } ]

[ { "id": "385603_1", "entity_ids": [ "385603_T2", "385603_T3" ] } ]

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[ { "id": "1548698__text", "type": "abstract", "text": [ "Refined crystal structure of ascorbate oxidase at 1.9 A resolution. \nThe crystal structure of the fully oxidized form of ascorbate oxidase (EC 1.10.3.3) from Zucchini has been refined at 1.90 A (1 A = 0.1 nm) resolution, using an energy-restrained least-squares refinement procedure. The refined model, which includes 8764 protein atoms, 9 copper atoms and 970 solvent molecules, has a crystallographic R-factor of 20.3% for 85,252 reflections between 8 and 1.90 A resolution. The root-mean-square deviation in bond lengths and bond angles from ideal values is 0.011 A and 2.99 degrees, respectively. The subunits of 552 residues (70,000 Mr) are arranged as tetramers with D2 symmetry. One of the dyads is realized by the crystallographic axis parallel to the c-axis giving one dimer in the asymmetric unit. The dimer related about this crystallographic axis is suggested as the dimer present in solution. Asn92 is the attachment site for one of the two N-linked sugar moieties, which has defined electron density for the N-linked N-acetyl-glucosamine ring. Each subunit is built up by three domains arranged sequentially on the polypeptide chain and tightly associated in space. The folding of all three domains is of a similar beta-barrel type and related to plastocyanin and azurin. An analysis of intra- and intertetramer hydrogen bond and van der Waals interactions is presented. Each subunit has four copper atoms bound as mononuclear and trinuclear species. The mononuclear copper has two histidine, a cysteine and a methionine ligand and represents the type-1 copper. It is located in domain 3. The bond lengths of the type-1 copper centre are comparable to the values for oxidized plastocyanin. The trinuclear cluster has eight histidine ligands symmetrically supplied from domain 1 and 3. It may be subdivided into a pair of copper atoms with histidine ligands whose ligating N-atoms (5 NE2 atoms and one ND1 atom) are arranged trigonal prismatic. The pair is the putative type-3 copper. The remaining copper has two histidine ligands and is the putative spectroscopic type-2 copper. Two oxygen atoms are bound to the trinuclear species as OH- or O2- and bridging the putative type-3 copper pair and as OH- or H2O bound to the putative type-2 copper trans to the copper pair. The bond lengths within the trinuclear copper site are similar to comparable binuclear model compounds. The putative binding site for the reducing substrate is close to the type-1 copper. (ABSTRACT TRUNCATED AT 400 WORDS) " ], "offsets": [ [ 0, 2508 ] ] } ]

[ { "id": "1548698_T1", "type": "Protein", "text": [ "ascorbate oxidase" ], "offsets": [ [ 29, 46 ] ], "normalized": [] }, { "id": "1548698_T2", "type": "Protein", "text": [ "ascorbate oxidase" ], "offsets": [ [ 121, 138 ] ], "normalized": [] }, { "id": "1548698_T3", "type": "Protein", "text": [ "plastocyanin" ], "offsets": [ [ 1261, 1273 ] ], "normalized": [] }, { "id": "1548698_T4", "type": "Protein", "text": [ "azurin" ], "offsets": [ [ 1278, 1284 ] ], "normalized": [] }, { "id": "1548698_T5", "type": "Entity", "text": [ "Asn92" ], "offsets": [ [ 906, 911 ] ], "normalized": [] } ]

[ { "id": "1548698_E1", "type": "Protein_amino_acid_glycosylation", "trigger": { "text": [ "N-linked sugar moieties" ], "offsets": [ [ 954, 977 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "1548698_T2" }, { "role": "Site", "ref_id": "1548698_T5" } ] } ]

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[ { "id": "15958184__text", "type": "abstract", "text": [ "A coupled fluorescent assay for histone methyltransferases. \nHistone methyltransferases (HMTs) catalyze the S-adenosylmethionine (AdoMet)-dependent methylation of lysines and arginines in the nucleosomal core histones H3 and H4 and the linker histone H1b. Methylation of these residues regulates either transcriptional activation or silencing, depending on the residue modified and its degree of methylation. Despite an intense interest in elucidating the functions of HMTs in transcriptional regulation, these enzymes have remained challenging to quantitatively assay. To characterize the substrate specificity of HMTs, we have developed a coupled-fluorescence-based assay for AdoMet-dependent methyltransferases. This assay utilizes S-adenosylhomocysteine hydrolase (SAHH) to hydrolyze the methyltransfer product S-adenosylhomocysteine (AdoHcy) to homocysteine (Hcy) and adenosine (Ado). The Hcy concentration is then determined through conjugation of its free sulfhydryl moiety to a thiol-sensitive fluorophore. Using this assay, we have determined the kinetic parameters for the methylation of a synthetic histone H3 peptide (corresponding to residues 1-15 of the native protein) by Schizosaccharomyces pombe CLR4, an H3 Lys-9-specific methyltransferase. The fluorescent SAHH-coupled assay allows rapid and facile determination of HMT kinetics and can be adapted to measure the enzymatic activity of a wide variety of AdoMet-dependent methyltransferases. " ], "offsets": [ [ 0, 1459 ] ] } ]

[ { "id": "15958184_T1", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 218, 220 ] ], "normalized": [] }, { "id": "15958184_T2", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 225, 227 ] ], "normalized": [] }, { "id": "15958184_T3", "type": "Protein", "text": [ "H1b" ], "offsets": [ [ 251, 254 ] ], "normalized": [] }, { "id": "15958184_T4", "type": "Protein", "text": [ "histone H3" ], "offsets": [ [ 1110, 1120 ] ], "normalized": [] }, { "id": "15958184_T5", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 1222, 1224 ] ], "normalized": [] }, { "id": "15958184_T6", "type": "Entity", "text": [ "Histone methyltransferases" ], "offsets": [ [ 61, 87 ] ], "normalized": [] }, { "id": "15958184_T7", "type": "Entity", "text": [ "HMTs" ], "offsets": [ [ 89, 93 ] ], "normalized": [] }, { "id": "15958184_T10", "type": "Entity", "text": [ "lysines" ], "offsets": [ [ 163, 170 ] ], "normalized": [] }, { "id": "15958184_T11", "type": "Entity", "text": [ "arginines" ], "offsets": [ [ 175, 184 ] ], "normalized": [] } ]

[ { "id": "15958184_E1", "type": "Positive_regulation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_E8" }, { "role": "Cause", "ref_id": "15958184_T7" } ] }, { "id": "15958184_E2", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_T1" }, { "role": "Site", "ref_id": "15958184_T11" } ] }, { "id": "15958184_E3", "type": "Positive_regulation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_E12" }, { "role": "Cause", "ref_id": "15958184_T7" } ] }, { "id": "15958184_E4", "type": "Positive_regulation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_E2" }, { "role": "Cause", "ref_id": "15958184_T7" } ] }, { "id": "15958184_E5", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_T1" }, { "role": "Site", "ref_id": "15958184_T10" } ] }, { "id": "15958184_E6", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_T2" }, { "role": "Site", "ref_id": "15958184_T11" } ] }, { "id": "15958184_E7", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_T2" }, { "role": "Site", "ref_id": "15958184_T10" } ] }, { "id": "15958184_E8", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_T3" }, { "role": "Site", "ref_id": "15958184_T11" } ] }, { "id": "15958184_E9", "type": "Positive_regulation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_E7" }, { "role": "Cause", "ref_id": "15958184_T7" } ] }, { "id": "15958184_E10", "type": "Positive_regulation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_E6" }, { "role": "Cause", "ref_id": "15958184_T7" } ] }, { "id": "15958184_E11", "type": "Positive_regulation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_E5" }, { "role": "Cause", "ref_id": "15958184_T7" } ] }, { "id": "15958184_E12", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "catalyze the S-adenosylmethionine (AdoMet)-dependent methylation" ], "offsets": [ [ 95, 159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_T3" }, { "role": "Site", "ref_id": "15958184_T10" } ] }, { "id": "15958184_E13", "type": "Protein_amino_acid_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1083, 1094 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "15958184_T4" } ] } ]

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