ArticleBiophysics reports2017
Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL.
Article in Biophysics reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Protein Secondary Structure Patterns in Short-Range Cross-Link Atlas.Angewandte Chemie (International ed. in English) · 2025Article
- Recent Developments in Data-Assisted Modeling of Flexible Proteins.Frontiers in molecular biosciences · 2021Review
- Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data.ACS central science · 2019Article
- ABA/ASB Omics 2018.Biophysical reviews · 2019Article
- Permanent Photodynamic Cholecystokinin 1 Receptor Activation: Dimer-to-Monomer Conversion.Cellular and molecular neurobiology · 2018Article
- Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking.Mass spectrometry reviewsReview
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Authors and funding
6 authors.
Funding
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Abstract
Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigid-body refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein-protein complexes, and is freely available at www.tanglab.org/resources.
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