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Public Library of Science, PLoS Computational Biology, 8(11), p. e1004362, 2015

DOI: 10.1371/journal.pcbi.1004362

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

Journal article published in 2015 by Jeffrey R. Johnson, Silvia D. Santos, Tasha Johnson, Ursula Pieper, Marta Strumillo ORCID, Omar Wagih ORCID, Andrej Sali, Nevan J. Krogan, Pedro Beltrao
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.