ArticleMolecular & cellular proteomics : MCP2016
Characterization of Dynamic UbR-Proteasome Subcomplexes by In vivo Cross-linking (X) Assisted Bimolecular Tandem Affinity Purification (XBAP) and Label-free Quantitation.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 39 citations in OpenAlex.
- Structures of dynamic interactors at native proteasomes by PhIX-MS and cryo-electron microscopy.Molecular cell · 2026Article
- In-situ cross-linking mass spectrometry reveals compartment-specific proteasomal interactions and structural heterogeneity.Nature communications · 2025Article
- Proximity labeling expansion microscopy (PL-ExM) evaluates interactome labeling techniques.Journal of materials chemistry. B · 2024Article
- Huntingtin contains an ubiquitin-binding domain and regulates lysosomal targeting of mitochondrial and RNA-binding proteins.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Proximity Labeling Expansion Microscopy (PL-ExM) resolves structure of the interactome.bioRxiv : the preprint server for biology · 2023Article
- Proximity Labeling in Plants.Annual review of plant biology · 2023Review
- E6AP AZUL interaction with UBQLN1/2 in cells, condensates, and an AlphaFold-NMR integrated structure.Structure (London, England : 1993) · 2023Article
- Proteasome substrate receptors and their therapeutic potential.Trends in biochemical sciences · 2022Review
- Developing a Targeted Quantitative Strategy for Sulfoxide-Containing MS-Cleavable Cross-Linked Peptides to Probe Conformational Dynamics of Protein Complexes.Analytical chemistry · 2022Article
- Characterization ofAnalytical chemistry · 2022Article
- Developing a Bimolecular Affinity Purification Strategy to Isolate 26S Proteasome Holocomplexes for Complex-Centric Proteomic Analysis.Analytical chemistry · 2021Article
- Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies.The FEBS journal · 2021Review
- Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Characterization of an A3G-VifMolecular & cellular proteomics : MCP · 2021Article
- Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches.Molecular & cellular proteomics : MCP · 2020Review
- Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Disabling the Protease DDI2 Attenuates the Transcriptional Activity of NRF1 and Potentiates Proteasome Inhibitor Cytotoxicity.International journal of molecular sciences · 2020Article
- Probing HMolecular & cellular proteomics : MCP · 2019Article
- Structure of hRpn10 Bound to UBQLN2 UBL Illustrates Basis for Complementarity between Shuttle Factors and Substrates at the Proteasome.Journal of molecular biology · 2019Article
- Efficient and robust proteome-wide approaches for cross-linking mass spectrometry.Nature protocols · 2018Article
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
Proteasomes are protein degradation machines that exist in cells as heterogeneous and dynamic populations. A group of proteins function as ubiquitin receptors (UbRs) that can recognize and deliver ubiquitinated substrates to proteasome complexes for degradation. Defining composition of proteasome complexes engaged with UbRs is critical to understand proteasome function. However, because of the dynamic nature of UbR interactions with the proteasome, it remains technically challenging to capture and isolate UbR-proteasome subcomplexes using conventional purification strategies. As a result, distinguishing the molecular differences among these subcomplexes remains elusive. We have developed a novel affinity purification strategy, in vivo cross-linking (X) assisted bimolecular tandem affinity purification strategy (XBAP), to effectively isolate dynamic UbR-proteasome subcomplexes and define their subunit compositions using label-free quantitative mass spectrometry. In this work, we have analyzed seven distinctive UbR-proteasome complexes and found that all of them contain the same type of the 26S holocomplex. However, selected UbRs interact with a group of proteasome interacting proteins that may link each UbR to specific cellular pathways. The compositional similarities and differences among the seven UbR-proteasome subcomplexes have provided new insights on functional entities of proteasomal degradation machineries. The strategy described here represents a general and useful proteomic tool for isolating and studying dynamic and heterogeneous protein subcomplexes in cells that have not been fully characterized.
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