Quantitative Structural Interpretation of Protein Crosslinks.
NRGXL
binary classification study
crosslinks
modeling
protein complexes
restraints
sampling
Journal
Structure (London, England : 1993)
ISSN: 1878-4186
Titre abrégé: Structure
Pays: United States
ID NLM: 101087697
Informations de publication
Date de publication:
07 01 2020
07 01 2020
Historique:
received:
06
05
2019
revised:
11
09
2019
accepted:
28
10
2019
pubmed:
23
11
2019
medline:
2
10
2020
entrez:
23
11
2019
Statut:
ppublish
Résumé
Chemical crosslinking, combined with mass spectrometry analysis, is a key source of information for characterizing the structure of large protein assemblies, in the context of molecular modeling. In most approaches, the interpretation is limited to simple spatial restraints, neglecting physico-chemical interactions between the crosslinker and the protein and their flexibility. Here we present a method, named NRGXL (new realistic grid for crosslinks), which models the flexibility of the crosslinker and the linked side-chains, by explicitly sampling many conformations. Also, the method can efficiently deal with overall protein dynamics. This method creates a physical model of the crosslinker and associated energy. A classifier based on it outperforms others, based on Euclidean distance or solvent-accessible distance and its efficiency makes it usable for validating 3D models from crosslinking data. NRGXL is freely available as a web server at: https://nrgxl.pasteur.fr.
Identifiants
pubmed: 31753619
pii: S0969-2126(19)30382-X
doi: 10.1016/j.str.2019.10.018
pii:
doi:
Substances chimiques
Cross-Linking Reagents
0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
75-82.e4Informations de copyright
Copyright © 2019 Elsevier Ltd. All rights reserved.