ArticleScientific reports2020
Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 32 citations in OpenAlex.
- Mapping the architecture of protein complexes inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Capturing the catalytic intermediates of parkin ubiquitination.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Chemical cross-linking and mass spectrometry enabled systems-level structural biology.Current opinion in structural biology · 2024Review
- Multidimensional Cross-Linking and Real-Time Informatics for Multiprotein Interaction Studies.Journal of proteome research · 2024Article
- Advances in mass spectrometry to unravel the structure and function of protein condensates.Nature protocols · 2023Review
- Probing Protein Dynamics in Neuronal Nitric Oxide Synthase by Quantitative Cross-Linking Mass Spectrometry.Biochemistry · 2023Article
- Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The Discovery of Ribosomal Protein bL31 fromInternational journal of molecular sciences · 2023Review
- Exploring an Alternative Cysteine-Reactive Chemistry to Enable Proteome-Wide PPI Analysis by Cross-Linking Mass Spectrometry.Analytical chemistry · 2023Article
- Interpretation of anomalously long crosslinks in ribosome crosslinking reveals the ribosome interaction in stationary phaseRSC chemical biology · 2022Article
- Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry.Chemical reviews · 2022Review
- Two-Dimensional Fractionation Method for Proteome-Wide Cross-Linking Mass Spectrometry Analysis.Analytical chemistry · 2022Article
- Promising Assays for Examining a Putative Role of Ribosomal Heterogeneity in COVID-19 Susceptibility and Severity.Life (Basel, Switzerland) · 2022Review
- Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Article
- Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs.Molecular omics · 2021Article
- Puf6 primes 60S pre-ribosome nuclear export at low temperature.Nature communications · 2021Article
- MS Annika: A New Cross-Linking Search Engine.Journal of proteome research · 2021Article
- Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology.Journal of proteome research · 2021Article
- Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective.Frontiers in molecular biosciences · 2021Article
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Authors and funding
5 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The ribosome is not only a highly complex molecular machine that translates the genetic information into proteins, but also an exceptional specimen for testing and optimizing cross-linking/mass spectrometry (XL-MS) workflows. Due to its high abundance, ribosomal proteins are frequently identified in proteome-wide XL-MS studies of cells or cell extracts. Here, we performed in-depth cross-linking of the E. coli ribosome using the amine-reactive cross-linker disuccinimidyl diacetic urea (DSAU). We analyzed 143 E. coli ribosomal structures, mapping a total of 10,771 intramolecular distances for 126 cross-link-pairs and 3,405 intermolecular distances for 97 protein pairs. Remarkably, 44% of intermolecular cross-links covered regions that have not been resolved in any high-resolution E. coli ribosome structure and point to a plasticity of cross-linked regions. We systematically characterized all cross-links and discovered flexible regions, conformational changes, and stoichiometric variations in bound ribosomal proteins, and ultimately remodeled 2,057 residues (15,794 atoms) in total. Our working model explains more than 95% of all cross-links, resulting in an optimized E. coli ribosome structure based on the cross-linking data obtained. Our study might serve as benchmark for conducting biochemical experiments on newly modeled protein regions, guided by XL-MS. Data are available via ProteomeXchange with identifier PXD018935.
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