SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation
Abstract A protein’s molecular interactions and post-translational modifications (PTMs), such as phosphorylation, can be co-dependent and reciprocally co-regulate each other. Although this interplay is central for many biological processes, a systematic method to simultaneously study assembly states...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-56303-0 |
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| author | Ella Doron-Mandel Benjamin J. Bokor Yanzhe Ma Lena A. Street Lauren C. Tang Ahmed A. Abdou Neel H. Shah George Rosenberger Marko Jovanovic |
| author_facet | Ella Doron-Mandel Benjamin J. Bokor Yanzhe Ma Lena A. Street Lauren C. Tang Ahmed A. Abdou Neel H. Shah George Rosenberger Marko Jovanovic |
| author_sort | Ella Doron-Mandel |
| collection | DOAJ |
| description | Abstract A protein’s molecular interactions and post-translational modifications (PTMs), such as phosphorylation, can be co-dependent and reciprocally co-regulate each other. Although this interplay is central for many biological processes, a systematic method to simultaneously study assembly states and PTMs from the same sample is critically missing. Here, we introduce SEC-MX (Size Exclusion Chromatography fractions MultipleXed), a global quantitative method combining Size Exclusion Chromatography and PTM-enrichment for simultaneous characterization of PTMs and assembly states. SEC-MX enhances throughput, allows phosphopeptide enrichment, and facilitates quantitative differential comparisons between biological conditions. Conducting SEC-MX on HEK293 and HCT116 cells, we generate a proof-of-concept dataset, mapping thousands of phosphopeptides and their assembly states. Our analysis reveals intricate relationships between phosphorylation events and assembly states and generates testable hypotheses for follow-up studies. Overall, we establish SEC-MX as a valuable tool for exploring protein functions and regulation beyond abundance changes. |
| format | Article |
| id | doaj-art-be88234c4bef4ae1ab8c5684e5d892b7 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-be88234c4bef4ae1ab8c5684e5d892b72025-02-02T12:31:42ZengNature PortfolioNature Communications2041-17232025-01-0116112010.1038/s41467-025-56303-0SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylationElla Doron-Mandel0Benjamin J. Bokor1Yanzhe Ma2Lena A. Street3Lauren C. Tang4Ahmed A. Abdou5Neel H. Shah6George Rosenberger7Marko Jovanovic8Department of Biological Sciences, Columbia UniversityDepartment of Biological Sciences, Columbia UniversityDepartment of Biological Sciences, Columbia UniversityDepartment of Biological Sciences, Columbia UniversityDepartment of Biological Sciences, Columbia UniversityDepartment of Biological Sciences, Columbia UniversityDepartment of Chemistry, Columbia UniversityDepartment of Systems Biology, Columbia UniversityDepartment of Biological Sciences, Columbia UniversityAbstract A protein’s molecular interactions and post-translational modifications (PTMs), such as phosphorylation, can be co-dependent and reciprocally co-regulate each other. Although this interplay is central for many biological processes, a systematic method to simultaneously study assembly states and PTMs from the same sample is critically missing. Here, we introduce SEC-MX (Size Exclusion Chromatography fractions MultipleXed), a global quantitative method combining Size Exclusion Chromatography and PTM-enrichment for simultaneous characterization of PTMs and assembly states. SEC-MX enhances throughput, allows phosphopeptide enrichment, and facilitates quantitative differential comparisons between biological conditions. Conducting SEC-MX on HEK293 and HCT116 cells, we generate a proof-of-concept dataset, mapping thousands of phosphopeptides and their assembly states. Our analysis reveals intricate relationships between phosphorylation events and assembly states and generates testable hypotheses for follow-up studies. Overall, we establish SEC-MX as a valuable tool for exploring protein functions and regulation beyond abundance changes.https://doi.org/10.1038/s41467-025-56303-0 |
| spellingShingle | Ella Doron-Mandel Benjamin J. Bokor Yanzhe Ma Lena A. Street Lauren C. Tang Ahmed A. Abdou Neel H. Shah George Rosenberger Marko Jovanovic SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation Nature Communications |
| title | SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation |
| title_full | SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation |
| title_fullStr | SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation |
| title_full_unstemmed | SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation |
| title_short | SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation |
| title_sort | sec mx an approach to systematically study the interplay between protein assembly states and phosphorylation |
| url | https://doi.org/10.1038/s41467-025-56303-0 |
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