Skip to Main content Skip to Navigation
Journal articles

Quantitative Structural Interpretation of Protein Crosslinks

Abstract : 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.
Complete list of metadatas

Cited literature [32 references]  Display  Hide  Download

https://hal-pasteur.archives-ouvertes.fr/pasteur-02369173
Contributor : Benjamin Bardiaux <>
Submitted on : Tuesday, November 10, 2020 - 7:17:51 PM
Last modification on : Friday, January 15, 2021 - 2:32:01 PM

File

accepted_version_figures.pdf
Files produced by the author(s)

Licence


Distributed under a Creative Commons Attribution - NonCommercial 4.0 International License

Identifiers

Collections

Citation

Isaac Filella-Merce, Benjamin Bardiaux, Michael Nilges, Guillaume Bouvier. Quantitative Structural Interpretation of Protein Crosslinks. Structure, Elsevier (Cell Press), 2020, 28 (1), pp.75-82. ⟨10.1016/j.str.2019.10.018⟩. ⟨pasteur-02369173⟩

Share

Metrics

Record views

115

Files downloads

139


Données de recherche

doi: web.