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Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics
Protein–protein interactions (PPIs) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components but mostly lack the context of cellular sta...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
National Academy of Sciences
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9546619/ https://www.ncbi.nlm.nih.gov/pubmed/36179048 http://dx.doi.org/10.1073/pnas.2117175119 |
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author | Ciuffa, Rodolfo Uliana, Federico Mannion, Jonathan Mehnert, Martin Tenev, Tencho Marulli, Cathy Satanowski, Ari Keller, Lena Maria Leone Rodilla Ramírez, Pilar Natalia Ori, Alessandro Gstaiger, Matthias Meier, Pascal Aebersold, Ruedi |
author_facet | Ciuffa, Rodolfo Uliana, Federico Mannion, Jonathan Mehnert, Martin Tenev, Tencho Marulli, Cathy Satanowski, Ari Keller, Lena Maria Leone Rodilla Ramírez, Pilar Natalia Ori, Alessandro Gstaiger, Matthias Meier, Pascal Aebersold, Ruedi |
author_sort | Ciuffa, Rodolfo |
collection | PubMed |
description | Protein–protein interactions (PPIs) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components but mostly lack the context of cellular states. However, the generation of context-dependent PPI networks is essential for structural and systems-level modeling of biological processes—a goal that remains an unsolved challenge. Here we describe an experimental/computational strategy to achieve a modeling of PPIs that considers contextual information. This strategy defines the composition, stoichiometry, temporal organization, and cellular requirements for the formation of target assemblies. We used this approach to generate an integrated model of the formation principles and architecture of a large signalosome, the TNF–receptor signaling complex (TNF-RSC). Overall, we show that the integration of systems- and structure-level information provides a generic, largely unexplored link between the modular proteome and cellular function. |
format | Online Article Text |
id | pubmed-9546619 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | National Academy of Sciences |
record_format | MEDLINE/PubMed |
spelling | pubmed-95466192022-10-08 Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics Ciuffa, Rodolfo Uliana, Federico Mannion, Jonathan Mehnert, Martin Tenev, Tencho Marulli, Cathy Satanowski, Ari Keller, Lena Maria Leone Rodilla Ramírez, Pilar Natalia Ori, Alessandro Gstaiger, Matthias Meier, Pascal Aebersold, Ruedi Proc Natl Acad Sci U S A Biological Sciences Protein–protein interactions (PPIs) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components but mostly lack the context of cellular states. However, the generation of context-dependent PPI networks is essential for structural and systems-level modeling of biological processes—a goal that remains an unsolved challenge. Here we describe an experimental/computational strategy to achieve a modeling of PPIs that considers contextual information. This strategy defines the composition, stoichiometry, temporal organization, and cellular requirements for the formation of target assemblies. We used this approach to generate an integrated model of the formation principles and architecture of a large signalosome, the TNF–receptor signaling complex (TNF-RSC). Overall, we show that the integration of systems- and structure-level information provides a generic, largely unexplored link between the modular proteome and cellular function. National Academy of Sciences 2022-09-30 2022-10-04 /pmc/articles/PMC9546619/ /pubmed/36179048 http://dx.doi.org/10.1073/pnas.2117175119 Text en Copyright © 2022 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by/4.0/This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Biological Sciences Ciuffa, Rodolfo Uliana, Federico Mannion, Jonathan Mehnert, Martin Tenev, Tencho Marulli, Cathy Satanowski, Ari Keller, Lena Maria Leone Rodilla Ramírez, Pilar Natalia Ori, Alessandro Gstaiger, Matthias Meier, Pascal Aebersold, Ruedi Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics |
title | Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics |
title_full | Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics |
title_fullStr | Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics |
title_full_unstemmed | Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics |
title_short | Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics |
title_sort | novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics |
topic | Biological Sciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9546619/ https://www.ncbi.nlm.nih.gov/pubmed/36179048 http://dx.doi.org/10.1073/pnas.2117175119 |
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