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...

Descripción completa

Detalles Bibliográficos
Autores principales: van Beusekom, Bart, Wezel, Natasja, Hekkelman, Maarten L., Perrakis, Anastassis, Emsley, Paul, Joosten, Robbie P.
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