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Protein structure as a means to triage proposed PTM sites

(2013) PROTEOMICS. 13(6). p.1028-1035
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
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.
Keywords
SURFACE, MOTIFS, RESIDUES, GLYCOSYLATION, LOCALIZATION, SEQUENCE, PREDICTION, INTRINSIC DISORDER, PHOSPHORYLATION SITES, Public repositories, KeyWords Plus: PROTEOMICS IDENTIFICATIONS DATABASE, PTM, Plant proteomics, Phosphorylation, Protein structure

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Citation

Please use this url to cite or link to this publication:

Chicago
Vandermarliere, Elien, and Lennart Martens. 2013. “Protein Structure as a Means to Triage Proposed PTM Sites.” Proteomics 13 (6): 1028–1035.
APA
Vandermarliere, E., & Martens, L. (2013). Protein structure as a means to triage proposed PTM sites. PROTEOMICS, 13(6), 1028–1035.
Vancouver
1.
Vandermarliere E, Martens L. Protein structure as a means to triage proposed PTM sites. PROTEOMICS. 2013;13(6):1028–35.
MLA
Vandermarliere, Elien, and Lennart Martens. “Protein Structure as a Means to Triage Proposed PTM Sites.” PROTEOMICS 13.6 (2013): 1028–1035. Print.
@article{3193811,
  abstract     = {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.},
  author       = {Vandermarliere, Elien and Martens, Lennart},
  issn         = {1615-9853},
  journal      = {PROTEOMICS},
  keyword      = {SURFACE,MOTIFS,RESIDUES,GLYCOSYLATION,LOCALIZATION,SEQUENCE,PREDICTION,INTRINSIC DISORDER,PHOSPHORYLATION SITES,Public repositories,KeyWords Plus: PROTEOMICS IDENTIFICATIONS DATABASE,PTM,Plant proteomics,Phosphorylation,Protein structure},
  language     = {eng},
  number       = {6},
  pages        = {1028--1035},
  title        = {Protein structure as a means to triage proposed PTM sites},
  url          = {http://dx.doi.org/10.1002/pmic.201200232},
  volume       = {13},
  year         = {2013},
}

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