ArticleBiochemistry2014
Middle-down mass spectrometry enables characterization of branched ubiquitin chains.
Article in Biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 91 citations in OpenAlex.
- The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitro.Life science alliance · 2025Article
- Understanding ubiquitination in neurodevelopment by integrating insights across space and time.Nature structural & molecular biology · 2025Review
- The Ubiquitin Tale: Current Strategies and Future Challenges.ACS pharmacology & translational science · 2024Review
- The emerging roles of non-canonical ubiquitination in proteostasis and beyond.The Journal of cell biology · 2024Review
- Decoding Ubiquitin Modifications by Mass Spectrometry.Advances in experimental medicine and biology · 2024Review
- Uncovering DUB Selectivity through an Ion Mobility-Based Assessment of Ubiquitin Chain Isomers.Analytical chemistry · 2023Article
- Proteomic approaches to study ubiquitinomics.Biochimica et biophysica acta. Gene regulatory mechanisms · 2023Review
- Triubiquitin Probes for Identification of Reader and Eraser Proteins of Branched Polyubiquitin Chains.ACS chemical biology · 2023Article
- Neutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes.Nature communications · 2023Article
- Assembly and disassembly of branched ubiquitin chains.Frontiers in molecular biosciences · 2023Review
- Getting to the Root of Branched Ubiquitin Chains: A Review of Current Methods and Functions.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture.Cell & bioscience · 2022Review
- A cryptic K48 ubiquitin chain binding site on UCH37 is required for its role in proteasomal degradation.eLife · 2022Article
- The Next Frontier: Translational Development of Ubiquitination, SUMOylation, and NEDDylation in Cancer.International journal of molecular sciences · 2022Review
- Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms.Mass spectrometry reviews · 2022Review
- The ubiquitin proteoform problem.Current opinion in chemical biology · 2021Review
- Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers.Cancers · 2021Review
- Emerging functions of branched ubiquitin chains.Cell discovery · 2021Review
- Tools for Decoding Ubiquitin Signaling in DNA Repair.Frontiers in cell and developmental biology · 2021Review
- Proteasome-Bound UCH37/UCHL5 Debranches Ubiquitin Chains to Promote Degradation.Molecular cell · 2020Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Protein ubiquitylation, one of the most prevalent post-translational modifications in eukaryotes, is involved in regulating nearly every cellular signaling pathway. The vast functional range of ubiquitylation has largely been attributed to the formation of a diverse array of polymeric ubiquitin (polyUb) chains. Methods that enable the characterization of these diverse chains are necessary to fully understand how differences in structure relate to function. Here, we describe a method for the detection of enzymatically derived branched polyUb conjugates in which a single Ub subunit is modified by two Ub molecules at distinct lysine residues. Using a middle-down mass spectrometry approach in which restricted trypsin-mediated digestion is coupled with mass spectrometric analysis, we characterize the polyUb chains produced by bacterial effector E3 ligases NleL (non-Lee-encoded effector ligase from enterohemorrhagic Escherichia coli O157:H7) and IpaH9.8 (from Shigella flexneri). Because Ub is largely intact after minimal trypsinolysis, multiple modifications on a single Ub moiety can be detected. Analysis of NleL- and IpaH9.8-derived polyUb chains reveals branch points are present in approximately 10% of the overall chain population. When unanchored, well-defined polyUb chains are added to reaction mixtures containing NleL, longer chains are more likely to be modified internally, forming branch points rather than extending from the end of the chain. These results suggest that middle-down mass spectrometry can be used to assess the extent to which branched polyUb chains are formed by various enzymatic systems and potentially evaluate the presence of these atypical conjugates in cell and tissue extracts.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.