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PLoS Comput Biol. 2015 Aug 27;11(8):e1004362. doi: 10.1371/journal.pcbi.1004362. eCollection 2015 Aug.

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.

Author information

1
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, United States of America.
2
Quantitative Cell Biology group, MRC Clinical Sciences Centre, Imperial College, London, United Kingdom.
3
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, University of California, San Francisco, San Francisco, California, United States of America; Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, University of California, San Francisco, San Francisco, California, United States of America.
4
European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany and European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom.
5
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, United States of America; Gladstone Institutes, San Francisco, California, United States of America.
6
European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany and European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom; iBiMED and Department of Health Sciences, University of Aveiro, Aveiro, Portugal.

Abstract

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.

PMID:
26312481
PMCID:
PMC4552029
DOI:
10.1371/journal.pcbi.1004362
[Indexed for MEDLINE]
Free PMC Article

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