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PubMed:11087743 JSONTXT

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GlyCosmos6-Glycan-Motif-Image

Id Subject Object Predicate Lexical cue image
T1 59-66 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T3 401-408 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T5 1055-1062 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T7 1198-1205 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T9 1592-1599 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T11 1601-1608 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T13 1860-1867 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T15 2012-2019 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO

sentences

Id Subject Object Predicate Lexical cue
T1 0-75 Sentence denotes Characterization of the stromal cell-derived factor-1alpha-heparin complex.
T2 76-181 Sentence denotes The binding of chemokines to glycosaminoglycans is thought to play a crucial role in chemokine functions.
T3 182-480 Sentence denotes It has recently been shown that stromal cell-derived factor-1alpha (SDF-1alpha), a CXC chemokine with potent anti-human immunodeficiency virus activity, binds to heparan sulfate through a typical consensus sequence for heparin recognition (BBXB, where B is a basic residue KHLK, amino acids 24-27).
T4 481-769 Sentence denotes Calculation of the accessible surface, together with the electrostatic potential of the SDF-1alpha dimer, revealed that other amino acids (Arg-41 and Lys-43) are found in the same surface area and contribute to the creation of a positively charged crevice, located at the dimer interface.
T5 770-905 Sentence denotes GRID calculations confirmed that this binding site will be the most energetically favored area for the interaction with sulfate groups.
T6 906-1063 Sentence denotes Site-directed mutagenesis and surface plasmon resonance-based binding assays were used to investigate the structural basis for SDF-1alpha binding to heparin.
T7 1064-1206 Sentence denotes Among the residues clustered in this basic surface area, Lys-24 and Lys-27 have dominant roles and are essential for interaction with heparin.
T8 1207-1328 Sentence denotes Amino acids Arg-41 and Lys-43 participate in the binding but are not strictly required for the interaction to take place.
T9 1329-1547 Sentence denotes Direct binding assays and competition analysis with monoclonal antibodies also permitted us to show that the N-terminal residue (Lys-1), an amino acid critical for receptor activation, is involved in complex formation.
T10 1548-1846 Sentence denotes Binding studies with selectively desulfated heparin, heparin oligosaccharides, and heparitinase-resistant heparan sulfate fragments showed that a minimum size of 12-14 monosaccharide units is required for efficient binding and that 2-O- and N-sulfate groups have a dominant role in the interaction.
T11 1847-1971 Sentence denotes Finally, the heparin-binding site was identified on the crystal structure of SDF-1alpha, and a docking study was undertaken.
T12 1972-2091 Sentence denotes During the energy minimization process, heparin lost its perfect ribbon shape and fitted the protein surface perfectly.
T13 2092-2249 Sentence denotes In the model, Lys-1, Lys-24, Lys-27, and Arg-41 were found to have the major role in binding a polysaccharide fragment consisting of 13 monosaccharide units.

GlyCosmos6-Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 59-66 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T2 59-66 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T3 401-408 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T4 401-408 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T5 1055-1062 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T6 1055-1062 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T7 1198-1205 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T8 1198-1205 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T9 1592-1599 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T10 1592-1599 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T11 1601-1608 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T12 1601-1608 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T13 1860-1867 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T14 1860-1867 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T15 2012-2019 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T16 2012-2019 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin

Glycosmos6-GlycoEpitope

Id Subject Object Predicate Lexical cue
T1 344-359 http://www.glycoepitope.jp/epitopes/EP0086 denotes heparan sulfate
T2 1654-1669 http://www.glycoepitope.jp/epitopes/EP0086 denotes heparan sulfate

Ab3P-abbreviations

Id Subject Object Predicate Lexical cue
SF0 250-260 ABBR denotes SDF-1alpha
LF0 214-248 ABBR denotes stromal cell-derived factor-1alpha
R0 LF0 SF0 ShortForm stromal cell-derived factor-1alpha,SDF-1alpha

mondo_disease

Id Subject Object Predicate Lexical cue mondo_id
T1 302-318 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094

HP-phenotype

Id Subject Object Predicate Lexical cue hp_id
T1 302-318 Phenotype denotes immunodeficiency HP:0002721

GlyCosmos15-HP

Id Subject Object Predicate Lexical cue hp_id
T1 302-318 Phenotype denotes immunodeficiency HP:0002721

GlyCosmos15-Sentences

Id Subject Object Predicate Lexical cue
T1 0-75 Sentence denotes Characterization of the stromal cell-derived factor-1alpha-heparin complex.
T2 76-181 Sentence denotes The binding of chemokines to glycosaminoglycans is thought to play a crucial role in chemokine functions.
T3 182-480 Sentence denotes It has recently been shown that stromal cell-derived factor-1alpha (SDF-1alpha), a CXC chemokine with potent anti-human immunodeficiency virus activity, binds to heparan sulfate through a typical consensus sequence for heparin recognition (BBXB, where B is a basic residue KHLK, amino acids 24-27).
T4 481-769 Sentence denotes Calculation of the accessible surface, together with the electrostatic potential of the SDF-1alpha dimer, revealed that other amino acids (Arg-41 and Lys-43) are found in the same surface area and contribute to the creation of a positively charged crevice, located at the dimer interface.
T5 770-905 Sentence denotes GRID calculations confirmed that this binding site will be the most energetically favored area for the interaction with sulfate groups.
T6 906-1063 Sentence denotes Site-directed mutagenesis and surface plasmon resonance-based binding assays were used to investigate the structural basis for SDF-1alpha binding to heparin.
T7 1064-1206 Sentence denotes Among the residues clustered in this basic surface area, Lys-24 and Lys-27 have dominant roles and are essential for interaction with heparin.
T8 1207-1328 Sentence denotes Amino acids Arg-41 and Lys-43 participate in the binding but are not strictly required for the interaction to take place.
T9 1329-1547 Sentence denotes Direct binding assays and competition analysis with monoclonal antibodies also permitted us to show that the N-terminal residue (Lys-1), an amino acid critical for receptor activation, is involved in complex formation.
T10 1548-1846 Sentence denotes Binding studies with selectively desulfated heparin, heparin oligosaccharides, and heparitinase-resistant heparan sulfate fragments showed that a minimum size of 12-14 monosaccharide units is required for efficient binding and that 2-O- and N-sulfate groups have a dominant role in the interaction.
T11 1847-1971 Sentence denotes Finally, the heparin-binding site was identified on the crystal structure of SDF-1alpha, and a docking study was undertaken.
T12 1972-2091 Sentence denotes During the energy minimization process, heparin lost its perfect ribbon shape and fitted the protein surface perfectly.
T13 2092-2249 Sentence denotes In the model, Lys-1, Lys-24, Lys-27, and Arg-41 were found to have the major role in binding a polysaccharide fragment consisting of 13 monosaccharide units.

GlyCosmos15-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 302-318 Disease denotes immunodeficiency MONDO:0021094

GlyCosmos15-Taxon

Id Subject Object Predicate Lexical cue db_id
T1 296-301 Organism denotes human 9606

GlyCosmos15-GlycoEpitope

Id Subject Object Predicate Lexical cue glycoepitope_id
T1 344-359 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes heparan sulfate http://www.glycoepitope.jp/epitopes/EP0086
T2 1654-1669 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes heparan sulfate http://www.glycoepitope.jp/epitopes/EP0086

GlyCosmos15-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 24-36 Body_part denotes stromal cell http://purl.obolibrary.org/obo/CL_0000499
T2 214-226 Body_part denotes stromal cell http://purl.obolibrary.org/obo/CL_0000499

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 296-301 OrganismTaxon denotes human 9606

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 24-36 Body_part denotes stromal cell http://purl.obolibrary.org/obo/CL_0000499
T2 214-226 Body_part denotes stromal cell http://purl.obolibrary.org/obo/CL_0000499

CL-cell

Id Subject Object Predicate Lexical cue cl_id
T1 24-36 Cell denotes stromal cell http://purl.obolibrary.org/obo/CL:0000499
T2 214-226 Cell denotes stromal cell http://purl.obolibrary.org/obo/CL:0000499