期刊
PROTEOMICS
卷 13, 期 6, 页码 1028-1035出版社
WILEY
DOI: 10.1002/pmic.201200232
关键词
Phosphorylation; Plant proteomics; Protein structure; PTM; Public repositories
资金
- IWT O&O Kinase Switch project
- Ghent University (Multidisciplinary Research Partnership Bioinformatics: from nucleotides to networks)
- PRIME-XS and ProteomeXchange projects
- European Union [262067, 260558]
PTMs such as phosphorylation are often important actors in protein regulation and recognition. These functions require both visibility and accessibility to other proteins; that the modification is located at the surface of the protein. Currently, many repositories provide information on PTMs but structural information is often lacking. This study, which focuses on phosphorylation sites available in UniProtKB/Swiss-Prot, illustrates that most phosphorylation sites are indeed found at the surface of the protein, but that some sites are found buried in the core of the protein. Several of these identified buried phosphorylation sites can easily become accessible upon small conformational changes while others would require the whole protein to unfold and are hence most unlikely modification sites. Subsequent analysis of phosphorylation sites available in PRIDE demonstrates that taking the structure of the protein into account would be a good guide in the identification of the actual phosphorylated positions in phophoproteomics experiments. This analysis illustrates that care must be taken when simply accepting the position of a PTM without first analyzing its position within the protein structure if the latter is available.
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