PubMed:33021626 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PubMed/sourceid/33021626","sourcedb":"PubMed","sourceid":"33021626","source_url":"https://www.ncbi.nlm.nih.gov/pubmed/33021626","text":"Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane.\nGlypican-1 and its heparan sulfate (HS) chains play important roles in modulating many biological processes including growth factor signaling. Glypican-1 is bound to a membrane surface via a glycosylphosphatidylinositol (GPI)-anchor. In this study, we used all-atom molecular modeling and simulation to explore the structure, dynamics, and interactions of GPI-anchored glypican-1, three HS chains, membranes, and ions. The folded glypican-1 core structure is stable, but has substantial degrees of freedom in terms of movement and orientation with respect to the membrane due to the long unstructured C-terminal region linking the core to the GPI-anchor. With unique structural features depending on the extent of sulfation, high flexibility of HS chains can promote multi-site interactions with surrounding molecules near and above the membrane. This study is a first step toward all-atom molecular modeling and simulation of the glycocalyx, as well as its modulation of interactions between growth factors and their receptors.","tracks":[{"project":"Glycosmos6-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":76,"end":92},"obj":"http://www.glycoepitope.jp/epitopes/EP0086"},{"id":"T2","span":{"begin":127,"end":142},"obj":"http://www.glycoepitope.jp/epitopes/EP0086"},{"id":"T3","span":{"begin":144,"end":146},"obj":"http://www.glycoepitope.jp/epitopes/EP0086"},{"id":"T4","span":{"begin":495,"end":497},"obj":"http://www.glycoepitope.jp/epitopes/EP0086"},{"id":"T5","span":{"begin":853,"end":855},"obj":"http://www.glycoepitope.jp/epitopes/EP0086"}],"attributes":[{"subj":"T1","pred":"source","obj":"Glycosmos6-GlycoEpitope"},{"subj":"T2","pred":"source","obj":"Glycosmos6-GlycoEpitope"},{"subj":"T3","pred":"source","obj":"Glycosmos6-GlycoEpitope"},{"subj":"T4","pred":"source","obj":"Glycosmos6-GlycoEpitope"},{"subj":"T5","pred":"source","obj":"Glycosmos6-GlycoEpitope"}]},{"project":"sentences","denotations":[{"id":"T1","span":{"begin":0,"end":107},"obj":"Sentence"},{"id":"T2","span":{"begin":108,"end":250},"obj":"Sentence"},{"id":"T3","span":{"begin":251,"end":341},"obj":"Sentence"},{"id":"T4","span":{"begin":342,"end":526},"obj":"Sentence"},{"id":"T5","span":{"begin":527,"end":762},"obj":"Sentence"},{"id":"T6","span":{"begin":763,"end":954},"obj":"Sentence"},{"id":"T7","span":{"begin":955,"end":1136},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T1","pred":"source","obj":"sentences"},{"subj":"T2","pred":"source","obj":"sentences"},{"subj":"T3","pred":"source","obj":"sentences"},{"subj":"T4","pred":"source","obj":"sentences"},{"subj":"T5","pred":"source","obj":"sentences"},{"subj":"T6","pred":"source","obj":"sentences"},{"subj":"T7","pred":"source","obj":"sentences"}]},{"project":"NCBITAXON","denotations":[{"id":"T1","span":{"begin":54,"end":59},"obj":"OrganismTaxon"}],"attributes":[{"id":"A1","pred":"db_id","subj":"T1","obj":"9606"},{"subj":"T1","pred":"source","obj":"NCBITAXON"}]},{"project":"Anatomy-UBERON","denotations":[{"id":"T1","span":{"begin":98,"end":106},"obj":"Body_part"},{"id":"T4","span":{"begin":276,"end":284},"obj":"Body_part"},{"id":"T7","span":{"begin":506,"end":515},"obj":"Body_part"},{"id":"T10","span":{"begin":671,"end":679},"obj":"Body_part"},{"id":"T13","span":{"begin":945,"end":953},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/GO_0016020"},{"id":"A2","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0000094"},{"id":"A3","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/GO_0016020"},{"id":"A5","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0000094"},{"id":"A6","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/GO_0016020"},{"id":"A8","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0000094"},{"id":"A9","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/GO_0016020"},{"id":"A11","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0000094"},{"id":"A12","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/GO_0016020"},{"id":"A14","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0000094"},{"id":"A15","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"subj":"T1","pred":"source","obj":"Anatomy-UBERON"},{"subj":"T4","pred":"source","obj":"Anatomy-UBERON"},{"subj":"T7","pred":"source","obj":"Anatomy-UBERON"},{"subj":"T10","pred":"source","obj":"Anatomy-UBERON"},{"subj":"T13","pred":"source","obj":"Anatomy-UBERON"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"Glycosmos6-GlycoEpitope","color":"#ec93b9","default":true},{"id":"sentences","color":"#93d3ec"},{"id":"NCBITAXON","color":"#eceb93"},{"id":"Anatomy-UBERON","color":"#d193ec"}]}]}}