Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol.
Covered surface
Glycan flexibility
Molecular dynamics
Unity
UnityMol
Journal
Methods (San Diego, Calif.)
ISSN: 1095-9130
Titre abrégé: Methods
Pays: United States
ID NLM: 9426302
Informations de publication
Date de publication:
15 02 2020
15 02 2020
Historique:
received:
01
03
2019
revised:
09
05
2019
accepted:
09
07
2019
pubmed:
16
7
2019
medline:
16
12
2020
entrez:
15
7
2019
Statut:
ppublish
Résumé
N-glycosylation is a post-translational modification heavily impacting protein functions. Some alterations of glycosylation, such as sialic acid hydrolysis, are related to protein dysfunction. Because of their high flexibility and the many reactive groups of the glycan chains, studying glycans with in vitro methods is a challenging task. Molecular dynamics is a useful tool and probably the only one in biology able to overcome this problem and gives access to conformational information through exhaustive sampling. To better decipher the impact of N-glycans, the analysis and visualization of their influence over time on protein structure is a prerequisite. We developed the Umbrella Visualization, a graphical method that assigns the glycan intrinsic flexibility during a molecular dynamics trajectory. The density plot generated by this method brought relevant informations regarding glycans dynamics and flexibility, but needs further development in order to integrate an accurate description of the protein topology and its interactions. We propose here to transform this analysis method into a visualization mode in UnityMol. UnityMol is a molecular editor, viewer and prototyping platform, coded in C#. The new representation of glycan chains presented in this study takes into account both the main positions adopted by each antenna of a glycan and their statistical relevance. By displaying the collected data on the protein surface, one is then able to investigate the protein/glycan interactions.
Identifiants
pubmed: 31302178
pii: S1046-2023(19)30028-3
doi: 10.1016/j.ymeth.2019.07.010
pmc: PMC7128144
pii:
doi:
Substances chimiques
Polysaccharides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
94-104Informations de copyright
Copyright © 2019 Elsevier Inc. All rights reserved.
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