ArticleThe Journal of biological chemistry2017
Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.
Article in The Journal of biological chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 58 citations in OpenAlex.
- In-situ cross-linking mass spectrometry reveals compartment-specific proteasomal interactions and structural heterogeneity.Nature communications · 2025Article
- Transient Cross-linking Mass Spectrometry: Taking Conformational Snapshots of Proteins.Analytical chemistry · 2025Article
- Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping.Nature communications · 2024Article
- Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology.JACS Au · 2024Review
- Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers.Briefings in bioinformatics · 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
- ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry.Bioinformatics (Oxford, England) · 2023Article
- Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders.The journal of physical chemistry. B · 2022Article
- Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers.Nature communications · 2022Article
- Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins.Frontiers in chemistry · 2021Review
- Recent Developments in Data-Assisted Modeling of Flexible Proteins.Frontiers in molecular biosciences · 2021Review
- PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system.Protein science : a publication of the Protein Society · 2020Article
- High-density chemical cross-linking for modeling protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Cellular Interactome Dynamics during Paclitaxel Treatment.Cell reports · 2019Article
- Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers.Nature communications · 2019Article
- Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.Journal of proteome research · 2019Article
- A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides.Nature communications · 2019Article
- On the necessity of an integrative approach to understand protein structural dynamics.Journal of Zhejiang University. Science. B · 2019Review
- Chemical cross-linking with mass spectrometry: a tool for systems structural biology.Current opinion in chemical biology · 2019Review
- Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology.Nature structural & molecular biology · 2018Review
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chemical cross-linking coupled with mass spectroscopy (CXMS) provides proximity information for the cross-linked residues and is used increasingly for modeling protein structures. However, experimentally identified cross-links are sometimes incompatible with the known structure of a protein, as the distance calculated between the cross-linked residues far exceeds the maximum length of the cross-linker. The discrepancies may persist even after eliminating potentially false cross-links and excluding intermolecular ones. Thus the "over-length" cross-links may arise from alternative excited-state conformation of the protein. Here we present a method and associated software DynaXL for visualizing the ensemble structures of multidomain proteins based on intramolecular cross-links identified by mass spectrometry with high confidence. Representing the cross-linkers and cross-linking reactions explicitly, we show that the protein excited-state structure can be modeled with as few as two over-length cross-links. We demonstrate the generality of our method with three systems: calmodulin, enzyme I, and glutamine-binding protein, and we show that these proteins alternate between different conformations for interacting with other proteins and ligands. Taken together, the over-length chemical cross-links contain valuable information about protein dynamics, and our findings here illustrate the relationship between dynamic domain movement and protein function.
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