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  The structural context of posttranslational modifications at a proteome-wide scale

Bludau, I., Willems, S., Zeng, W.-F., Strauss, M. T., Hansen, F. M., Tanzer, M. C., et al. (2022). The structural context of posttranslational modifications at a proteome-wide scale. PLoS Biology, 20(5): e3001636. doi:10.1371/journal.pbio.3001636.

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 Creators:
Bludau, Isabell1, Author           
Willems, Sander1, Author           
Zeng, Wen-Feng1, Author           
Strauss, Maximilian T.2, Author
Hansen, Fynn M.1, Author           
Tanzer, Maria C.1, Author           
Karayel, Ozge1, Author           
Schulman, Brenda A.3, Author           
Mann, Matthias1, Author           
Affiliations:
1Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565159              
2external, ou_persistent22              
3Schulman, Brenda / Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Max Planck Society, ou_2466699              

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Free keywords: AMINO-ACID; PHOSPHORYLATION; UBIQUITINATION; PREDICTION; POWERFUL; DATABASE; KINASE; TOOLSBiochemistry & Molecular Biology; Life Sciences & Biomedicine - Other Topics;
 Abstract: The recent revolution in computational protein structure prediction provides folding models for entire proteomes, which can now be integrated with large-scale experimental data. Mass spectrometry (MS)-based proteomics has identified and quantified tens of thousands of posttranslational modifications (PTMs), most of them of uncertain functional relevance. In this study, we determine the structural context of these PTMs and investigate how this information can be leveraged to pinpoint potential regulatory sites. Our analysis uncovers global patterns of PTM occurrence across folded and intrinsically disordered regions. We found that this information can help to distinguish regulatory PTMs from those marking improperly folded proteins. Interestingly, the human proteome contains thousands of proteins that have large folded domains linked by short, disordered regions that are strongly enriched in regulatory phosphosites. These include well-known kinase activation loops that induce protein conformational changes upon phosphorylation. This regulatory mechanism appears to be widespread in kinases but also occurs in other protein families such as solute carriers. It is not limited to phosphorylation but includes ubiquitination and acetylation sites as well. Furthermore, we performed three-dimensional proximity analysis, which revealed examples of spatial coregulation of different PTM types and potential PTM crosstalk. To enable the community to build upon these first analyses, we provide tools for 3D visualization of proteomics data and PTMs as well as python libraries for data accession and processing.

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Language(s): eng - English
 Dates: 2022-05-16
 Publication Status: Published online
 Pages: 23
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Degree: -

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Title: PLoS Biology
  Other : PLoS Biol.
Source Genre: Journal
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Publ. Info: San Francisco, California, US : Public Library of Science
Pages: - Volume / Issue: 20 (5) Sequence Number: e3001636 Start / End Page: - Identifier: ISSN: 1544-9173
CoNE: https://pure.mpg.de/cone/journals/resource/111056649444170