Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
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 p...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2015-08-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1004362 |
| _version_ | 1819259779483172864 |
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| author | Jeffrey R Johnson Silvia D Santos Tasha Johnson Ursula Pieper Marta Strumillo Omar Wagih Andrej Sali Nevan J Krogan Pedro Beltrao |
| author_facet | Jeffrey R Johnson Silvia D Santos Tasha Johnson Ursula Pieper Marta Strumillo Omar Wagih Andrej Sali Nevan J Krogan Pedro Beltrao |
| author_sort | Jeffrey R Johnson |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-23T19:15:26Z |
| format | Article |
| id | doaj.art-4f6ec5926f1e44e0a3e36ee995811a29 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-23T19:15:26Z |
| publishDate | 2015-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-4f6ec5926f1e44e0a3e36ee995811a292022-12-21T17:34:19ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582015-08-01118e100436210.1371/journal.pcbi.1004362Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.Jeffrey R JohnsonSilvia D SantosTasha JohnsonUrsula PieperMarta StrumilloOmar WagihAndrej SaliNevan J KroganPedro BeltraoThe 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.https://doi.org/10.1371/journal.pcbi.1004362 |
| spellingShingle | Jeffrey R Johnson Silvia D Santos Tasha Johnson Ursula Pieper Marta Strumillo Omar Wagih Andrej Sali Nevan J Krogan Pedro Beltrao Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PLoS Computational Biology |
| title | Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. |
| title_full | Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. |
| title_fullStr | Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. |
| title_full_unstemmed | Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. |
| title_short | Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. |
| title_sort | prediction of functionally important phospho regulatory events in xenopus laevis oocytes |
| url | https://doi.org/10.1371/journal.pcbi.1004362 |
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