ArticlePLoS biology2022
The structural context of posttranslational modifications at a proteome-wide scale.
Article in PLoS biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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77 citing papers in PubMed, 120 citations in OpenAlex.
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- SPSignal: a web tool for structure-assisted prediction of nuclear localization and nuclear export signals in proteins.Nucleic acids research · 2026Article
- Analysis of Confounding Factors in Reactive Cysteine Profiling Reveals Enhanced Chromatin-Protein Association via CDK7 Inhibition by THZ1.ACS chemical biology · 2026Article
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Article
- StrucPTM: a database of structurally validated protein modifications and their conformational variation.Bioinformatics (Oxford, England) · 2026Article
- Post-translational modifications of silk proteins.RSC chemical biology · 2026Review
- Chiral methionine oxidation reagents reveal stereospecific proteome modifications.bioRxiv : the preprint server for biology · 2026Article
- Methods for studying the effects of phosphorylation patterns in proteins.Biochemical Society transactions · 2026Review
- Post-Translational Modifications in Animal Circadian Clocks.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Biocompatible ligand balancing in transition metal coordination enables benign in-cell protein arylation.Nature chemistry · 2026Article
- A Peptide-Centric DIA-NN Reanalysis Uncovers Structurally Coherent Salivary Signatures of Type 2 Diabetes.International journal of molecular sciences · 2026Article
- High-throughput chemical proteomics workflow for profiling protein citrullination dynamics.Nature communications · 2026Article
- The Axon as a Self-Modifying Computational System: Autonomous Inference, Adaptive Propagation, and AI-Enabled Mechanistic Insight.International journal of molecular sciences · 2026Review
- TheJournal of proteome research · 2026Article
- Recent Advances in Polyoxometalates Targeting Proteins Associated with Alzheimer's Disease: From Molecular Mechanisms to Therapeutic Applications.International journal of molecular sciences · 2026Review
- Atlas of lysine acetylation in the mouse.bioRxiv : the preprint server for biology · 2026Article
- Post-Translational Modifications in Respiratory Virus Infection: Recent Insights into the Development of In Vitro Models.International journal of molecular sciences · 2025Review
17 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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