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PLoS Comput Biol 2015 Aug 27;118:e1004362. doi: 10.1371/journal.pcbi.1004362.
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Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.

Johnson JR , Santos SD , Johnson T , Pieper U , Strumillo M , Wagih O , Sali A , Krogan NJ , Beltrao P .

The African clawed frog Xenopus laevis is an important model organism for studies in developmental and cell biology, including cell-signaling. However, our knowledge of X. laevis protein post-translational modifications remains scarce. Here, we used a mass spectrometry-based approach to survey the phosphoproteome of this species, compiling a list of 2636 phosphosites. We used structural information and phosphoproteomic data for 13 other species in order to predict functionally important phospho-regulatory events. We found that the degree of conservation of phosphosites across species is predictive of sites with known molecular function. In addition, we predicted kinase-protein interactions for a set of cell-cycle kinases across all species. The degree of conservation of kinase-protein interactions was found to be predictive of functionally relevant regulatory interactions. Finally, using comparative protein structure models, we find that phosphosites within structured domains tend to be located at positions with high conformational flexibility. Our analysis suggests that a small class of phosphosites occurs in positions that have the potential to regulate protein conformation.

PubMed ID: 26312481
PMC ID: PMC4552029
Article link: PLoS Comput Biol
Grant support: [+]

Species referenced: Xenopus laevis
Genes referenced: ap3d1 atr aurka aurkb cad casp1 cct3 cdk1 cdk2 cdk7 chek1 dnm1l eef1b2 eif5b gbf1 gsk3b hsp90ab1 leo1 lig1 mcm2 ndp nek2 nek6 nek9 nup98 pgm1 plk1 plk2 plk3 prkar2a ran rnf113a rpl12 rplp0 rps6 rps6kb1 sec61b supt5h tpr ttk utp18 ybx1 ybx2

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References [+] :
Baker, Modification site localization scoring integrated into a search engine. 2011, Pubmed