ArticleNature methods2016
Automated structure modeling of large protein assemblies using crosslinks as distance restraints.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Dynamic positioning of Rpc34 winged helix in RNA polymerase III elongation complex for its stability with implications for reinitiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry.Nature communications · 2026Article
- Transient Cross-linking Mass Spectrometry: Taking Conformational Snapshots of Proteins.Analytical chemistry · 2025Article
- Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology.JACS Au · 2024Review
- Integrative structural modeling of macromolecular complexes using Assembline.Nature protocols · 2022Review
- Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs.Molecular omics · 2021Article
- Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens.Diagnostics (Basel, Switzerland) · 2021Review
- Automatic Bayesian Weighting for SAXS Data.Frontiers in molecular biosciences · 2021Article
- High-density chemical cross-linking for modeling protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.Structure (London, England : 1993) · 2019Article
- Interpretation of medium resolution cryoEM maps of multi-protein complexes.Current opinion in structural biology · 2019Review
- Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data.ACS central science · 2019Article
- On the necessity of an integrative approach to understand protein structural dynamics.Journal of Zhejiang University. Science. B · 2019Review
- Development of R7BP inhibitors through cross-linking coupled mass spectrometry and integrated modeling.Communications biology · 2019Article
- Rapid Mapping of Protein Interactions Using Tag-Transfer Photocrosslinkers.Angewandte Chemie (International ed. in English) · 2018Article
- Efficient and robust proteome-wide approaches for cross-linking mass spectrometry.Nature protocols · 2018Article
- Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology.Nature structural & molecular biology · 2018Review
- Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry.Structure (London, England : 1993) · 2018Article
- Protein Tertiary Structure by Crosslinking/Mass Spectrometry.Trends in biochemical sciences · 2018Review
- Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology.Analytical chemistry · 2018Review
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Authors and funding
11 authors.
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Abstract
Crosslinking mass spectrometry is increasingly used for structural characterization of multisubunit protein complexes. Chemical crosslinking captures conformational heterogeneity, which typically results in conflicting crosslinks that cannot be satisfied in a single model, making detailed modeling a challenging task. Here we introduce an automated modeling method dedicated to large protein assemblies ('XL-MOD' software is available at http://aria.pasteur.fr/supplementary-data/x-links) that (i) uses a form of spatial restraints that realistically reflects the distribution of experimentally observed crosslinked distances; (ii) automatically deals with ambiguous and/or conflicting crosslinks and identifies alternative conformations within a Bayesian framework; and (iii) allows subunit structures to be flexible during conformational sampling. We demonstrate our method by testing it on known structures and available crosslinking data. We also crosslinked and modeled the 17-subunit yeast RNA polymerase III at atomic resolution; the resulting model agrees remarkably well with recently published cryoelectron microscopy structures and provides additional insights into the polymerase structure.
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