ArticlePloS one2013
Structural propensities of human ubiquitination sites: accessibility, centrality and local conformation.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- CLASPP: A unified model for predicting post-translational modifications.PLoS computational biology · 2026Article
- Structural proteomics reveals that misfolded nascent proteins expose buried lysines for ubiquitination and rapid proteasomal degradation.Cell reports · 2026Article
- CLASPP: A unified model for predicting post-translational modifications.bioRxiv : the preprint server for biology · 2026Article
- RF-MaloSite and DL-Malosite: Methods based on random forest and deep learning to identify malonylation sites.Computational and structural biotechnology journal · 2020Article
- DephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites.Scientific reports · 2016Article
- Nonspecific yet decisive: Ubiquitination can affect the native-state dynamics of the modified protein.Protein science : a publication of the Protein Society · 2015Article
- Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.PloS one · 2015Article
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4 authors.
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Abstract
The existence and function of most proteins in the human proteome are regulated by the ubiquitination process. To date, tens of thousands human ubiquitination sites have been identified from high-throughput proteomic studies. However, the mechanism of ubiquitination site selection remains elusive because of the complicated sequence pattern flanking the ubiquitination sites. In this study, we perform a systematic analysis of 1,330 ubiquitination sites in 505 protein structures and quantify the significantly high accessibility and unexpectedly high centrality of human ubiquitination sites. Further analysis suggests that the higher centrality of ubiquitination sites is associated with the multi-functionality of ubiquitination sites, among which protein-protein interaction sites are common targets of ubiquitination. Moreover, we demonstrate that ubiquitination sites are flanked by residues with non-random local conformation. Finally, we provide quantitative and unambiguous evidence that most of the structural propensities contain specific information about ubiquitination site selection that is not represented by the sequence pattern. Therefore, the hypothesis about the structural level of the ubiquitination site selection mechanism has been substantially approved.
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