ArticleBiophysics reports2015
Visualizing the Ensemble Structures of Protein Complexes Using Chemical Cross-Linking Coupled with Mass Spectrometry.
Article in Biophysics reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Going high-throughput: Dynamic conformations and interactionsMagnetic resonance letters · 2027Review
- In-situ cross-linking mass spectrometry reveals compartment-specific proteasomal interactions and structural heterogeneity.Nature communications · 2025Article
- Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells.Nature communications · 2024Article
- Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping.Nature communications · 2024Article
- Characterization of β-Barrel Outer Membrane Proteins and Their Interactions with Chaperones by Chemical-Crosslinking Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Fast cross-linking by DOPA2 promotes the capturing of a stereospecific protein complex over nonspecific encounter complexes.Biophysics reports · 2022Article
- Specific binding of Hsp27 and phosphorylated Tau mitigates abnormal Tau aggregation-induced pathology.eLife · 2022Article
- Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders.The journal of physical chemistry. B · 2022Article
- The mouse nicotinamide mononucleotide adenylyltransferase chaperones diverse pathological amyloid client proteins.The Journal of biological chemistry · 2022Article
- Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers.Nature communications · 2022Article
- Recent Developments in Data-Assisted Modeling of Flexible Proteins.Frontiers in molecular biosciences · 2021Review
- Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers.Nature communications · 2019Article
- On the necessity of an integrative approach to understand protein structural dynamics.Journal of Zhejiang University. Science. B · 2019Review
- Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology.Analytical chemistry · 2018Review
- Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.The Journal of biological chemistry · 2017Article
- Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL.Biophysics reports · 2017Article
- Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations.Scientific reports · 2016Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
graphical abstractABSTRACT: Chemical cross-linking coupled with mass spectrometry (CXMS) identifies protein residues that are close in space, and has been increasingly used for modeling the structures of protein complexes. Here we show that a single structure is usually sufficient to account for the intermolecular cross-links identified for a stable complex with sub-µmol/L binding affinity. In contrast, we show that the distance between two cross-linked residues in the different subunits of a transient or fleeting complex may exceed the maximum length of the cross-linker used, and the cross-links cannot be fully accounted for with a unique complex structure. We further show that the seemingly incompatible cross-links identified with high confidence arise from alternative modes of protein-protein interactions. By converting the intermolecular cross-links to ambiguous distance restraints, we established a rigid-body simulated annealing refinement protocol to seek the minimum set of conformers collectively satisfying the CXMS data. Hence we demonstrate that CXMS allows the depiction of the ensemble structures of protein complexes and elucidates the interaction dynamics for transient and fleeting complexes.
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