ArticleMolecular & cellular proteomics : MCP2012
Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling.
Article in Molecular & cellular proteomics : MCP, 2012. 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, 59 citations in OpenAlex.
- New Scaffolds of Proteasome Inhibitors: Boosting Anticancer Potential by Exploiting the Synergy of In Silico and In Vitro Methodologies.Pharmaceuticals (Basel, Switzerland) · 2023Article
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- 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
- Exploring Spacer Arm Structures for Designs of Asymmetric Sulfoxide-Containing MS-Cleavable Cross-Linkers.Analytical chemistry · 2020Article
- 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
- Probing HMolecular & cellular proteomics : MCP · 2019Article
- Evaluation of Different Stationary Phases in the Separation of Inter-Cross-Linked Peptides.Journal of proteome research · 2019Article
- A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein-protein interactions.Nature protocols · 2018Article
- Development of a Novel Sulfoxide-Containing MS-Cleavable Homobifunctional Cysteine-Reactive Cross-Linker for Studying Protein-Protein Interactions.Analytical chemistry · 2018Article
- Protein Tertiary Structure by Crosslinking/Mass Spectrometry.Trends in biochemical sciences · 2018Review
- Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology.Analytical chemistry · 2018Review
- Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome.Molecular & cellular proteomics : MCP · 2017Article
- In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075.Nature communications · 2016Article
- Developing a Multiplexed Quantitative Cross-Linking Mass Spectrometry Platform for Comparative Structural Analysis of Protein Complexes.Analytical chemistry · 2016Article
- Article
- Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein-Protein Interactions.Analytical chemistry · 2016Article
- Article
- Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology.Molecular & cellular proteomics : MCP · 2016Article
- Mass Spectrometry: A Technique of Many Faces.Quarterly reviews of biophysics · 2016Review
- Gln40 deamidation blocks structural reconfiguration and activation of SCF ubiquitin ligase complex by Nedd8.Nature communications · 2015Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Structural characterization of proteasome complexes is an essential step toward understanding the ubiquitin-proteasome system. Currently, high resolution structures are not available for the 26S proteasome holocomplex as well as its subcomplex, the 19S regulatory particle (RP). Here we have employed a novel integrated strategy combining chemical cross-linking with multistage tandem mass spectrometry to define the proximity of subunits within the yeast 19S RP to elucidate its topology. This has resulted in the identification of 174 cross-linked peptides of the yeast 19S RP, representing 43 unique lysine-lysine linkages within 24 nonredundant pair-wise subunit interactions. To map the spatial organization of the 19S RP, we have developed and utilized a rigorous probabilistic framework to derive maximum likelihood (ML) topologies based on cross-linked peptides determined from our analysis. Probabilistic modeling of the yeast 19S AAA-ATPase ring (i.e., Rpt1-6) has produced an ML topology that is in excellent agreement with known topologies of its orthologs. In addition, similar analysis was carried out on the 19S lid subcomplex, whose predicted ML topology corroborates recently reported electron microscopy studies. Together, we have demonstrated the effectiveness and potential of probabilistic modeling for unraveling topologies of protein complexes using cross-linking data. This report describes the first study of the 19S RP topology using a new integrated strategy combining chemical cross-linking, mass spectrometry, and probabilistic modeling. Our results have provided a solid foundation to advance our understanding of the 19S RP architecture at peptide level resolution. Furthermore, our methodology developed here is a valuable proteomic tool that can be generalized for elucidating the structures of protein complexes.
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Registered trials
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