Cargando…
Building and rebuilding N-glycans in protein structure models
N-Glycosylation is one of the most common post-translational modifications and is implicated in, for example, protein folding and interaction with ligands and receptors. N-Glycosylation trees are complex structures of linked carbohydrate residues attached to asparagine residues. While carbohydrates...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465985/ https://www.ncbi.nlm.nih.gov/pubmed/30988258 http://dx.doi.org/10.1107/S2059798319003875 |
_version_ | 1783411005860085760 |
---|---|
author | van Beusekom, Bart Wezel, Natasja Hekkelman, Maarten L. Perrakis, Anastassis Emsley, Paul Joosten, Robbie P. |
author_facet | van Beusekom, Bart Wezel, Natasja Hekkelman, Maarten L. Perrakis, Anastassis Emsley, Paul Joosten, Robbie P. |
author_sort | van Beusekom, Bart |
collection | PubMed |
description | N-Glycosylation is one of the most common post-translational modifications and is implicated in, for example, protein folding and interaction with ligands and receptors. N-Glycosylation trees are complex structures of linked carbohydrate residues attached to asparagine residues. While carbohydrates are typically modeled in protein structures, they are often incomplete or have the wrong chemistry. Here, new tools are presented to automatically rebuild existing glycosylation trees, to extend them where possible, and to add new glycosylation trees if they are missing from the model. The method has been incorporated in the PDB-REDO pipeline and has been applied to build or rebuild 16 452 carbohydrate residues in 11 651 glycosylation trees in 4498 structure models, and is also available from the PDB-REDO web server. With better modeling of N-glycosylation, the biological function of this important modification can be better and more easily understood. |
format | Online Article Text |
id | pubmed-6465985 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-64659852019-04-19 Building and rebuilding N-glycans in protein structure models van Beusekom, Bart Wezel, Natasja Hekkelman, Maarten L. Perrakis, Anastassis Emsley, Paul Joosten, Robbie P. Acta Crystallogr D Struct Biol Research Papers N-Glycosylation is one of the most common post-translational modifications and is implicated in, for example, protein folding and interaction with ligands and receptors. N-Glycosylation trees are complex structures of linked carbohydrate residues attached to asparagine residues. While carbohydrates are typically modeled in protein structures, they are often incomplete or have the wrong chemistry. Here, new tools are presented to automatically rebuild existing glycosylation trees, to extend them where possible, and to add new glycosylation trees if they are missing from the model. The method has been incorporated in the PDB-REDO pipeline and has been applied to build or rebuild 16 452 carbohydrate residues in 11 651 glycosylation trees in 4498 structure models, and is also available from the PDB-REDO web server. With better modeling of N-glycosylation, the biological function of this important modification can be better and more easily understood. International Union of Crystallography 2019-04-04 /pmc/articles/PMC6465985/ /pubmed/30988258 http://dx.doi.org/10.1107/S2059798319003875 Text en © van Beusekom et al. 2019 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Research Papers van Beusekom, Bart Wezel, Natasja Hekkelman, Maarten L. Perrakis, Anastassis Emsley, Paul Joosten, Robbie P. Building and rebuilding N-glycans in protein structure models |
title | Building and rebuilding N-glycans in protein structure models |
title_full | Building and rebuilding N-glycans in protein structure models |
title_fullStr | Building and rebuilding N-glycans in protein structure models |
title_full_unstemmed | Building and rebuilding N-glycans in protein structure models |
title_short | Building and rebuilding N-glycans in protein structure models |
title_sort | building and rebuilding n-glycans in protein structure models |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465985/ https://www.ncbi.nlm.nih.gov/pubmed/30988258 http://dx.doi.org/10.1107/S2059798319003875 |
work_keys_str_mv | AT vanbeusekombart buildingandrebuildingnglycansinproteinstructuremodels AT wezelnatasja buildingandrebuildingnglycansinproteinstructuremodels AT hekkelmanmaartenl buildingandrebuildingnglycansinproteinstructuremodels AT perrakisanastassis buildingandrebuildingnglycansinproteinstructuremodels AT emsleypaul buildingandrebuildingnglycansinproteinstructuremodels AT joostenrobbiep buildingandrebuildingnglycansinproteinstructuremodels |