The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Systematic Functional Prioritization of Protein Posttranslational Modifications
Open accessAbstract
Protein function is often regulated by post-translational modifications (PTMs) and recent advances in mass-spectrometry have resulted in an exponential increase in PTM identification. However, the functional significance of the vast majority of these modifications remains unknown. To address this problem, we compiled nearly 200,000 phosphorylation, acetylation and ubiquitination sites from 11 eukaryotic species, including 2,500 novel ubiquitylation sites for S. cerevisiae. We developed methods to prioritize the functional relevance of these PTMs by predicting those that likely participate in cross-regulatory events, regulate domain activity or mediate protein-protein interactions. PTM conservation within domain families identifies regulatory ‘hot-spots’ that overlap with functionally important regions, a concept we experimentally validated on the HSP70 domain family. Finally, our analysis of the evolution of PTM regulation highlights potential routes for neutral drift in regulatory interactions and suggests that only a fraction of modification sites are likely to have a significant biological role.
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Cites
Lysine acetylation targets protein complexes and co-regulates major cellular functions
Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., & Mann, M. (2009) · Science · doi:10.1126/science.1175371 · Cited by 4,040
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Function and regulation of cullin–RING ubiquitin ligases
Petroski, M. D., & Deshaies, R. J. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1547 · Cited by 2,148
HSP90 at the hub of protein homeostasis: emerging mechanistic insights
Taipale, M., Jarosz, D. F., & Lindquist, S. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2918 · Cited by 1,818
Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006) · Nature Biotechnology · doi:10.1038/nbt1240 · Cited by 1,577
Self-citationCrystal structure of an Hsp90–nucleotide–p23/Sba1 closed chaperone complex
Ali, M. M. U., Roe, S. M., Vaughan, C. K., Meyer, P., Panaretou, B., Piper, P. W., Prodromou, C., & Pearl, L. H. (2006) · Nature · doi:10.1038/nature04716 · Cited by 962
Evolution at Two Levels: On Genes and Form
Carroll, S. B. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030245 · Cited by 882
Linear motifs: Evolutionary interaction switches
Neduva, V., & Russell, R. B. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.04.005 · Cited by 352
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species
Beltrao, P., Trinidad, J. C., Fiedler, D., Roguev, A., Lim, W. A., Shokat, K. M., Burlingame, A. L., & Krogan, N. J. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000134 · Cited by 188
Self-citationConformational Switching of the Molecular Chaperone Hsp90 via Regulated Phosphorylation
Soroka, J., Wandinger, S. K., Mäusbacher, N., Schreiber, T., Richter, K., Daub, H., & Buchner, J. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.12.031 · Cited by 139 · cited 1×
“Consistent with these ideas, Soroka and colleagues validated this prediction by demonstrating that the 600–610 region of the yeast HSP90 is in fact regulated by Ppt1 and that phosphorylation of this region has the potential to regulate HSP90 function (Soroka et al., 2012).”
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Cited by
The growing landscape of lysine acetylation links metabolism and cell signalling
Choudhary, C., Weinert, B. T., Nishida, Y., Verdin, E., & Mann, M. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3841 · Cited by 1,324
The functional landscape of the human phosphoproteome
Ochoa, D., Jarnuczak, A. F., Viéitez, C., Gehre, M., Soucheray, M., Mateus, A., Kleefeldt, A. A., Hill, A., Garcia-Alonso, L., Stein, F., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0344-3 · Cited by 491
Self-citationZhong, Q., Xiao, X., Qiu, Y., Xu, Z., Chen, C., Chong, B., Zhao, X., Hai, S., Li, S., An, Z., et al. (2023) · MedComm · doi:10.1002/mco2.261 · Cited by 442
Pejaver, V., Hsu, W., Xin, F., Dunker, A. K., Uversky, V. N., & Radivojac, P. (2014) · Protein Science · doi:10.1002/pro.2494 · Cited by 349
Evolution of heat‐shock protein expression underlying adaptive responses to environmental stress
Chen, B., Feder, M. E., & Kang, L. (2018) · Molecular Ecology · doi:10.1111/mec.14769 · Cited by 267
Metadata
- Authors
- Beltrao, P., Albanèse, V., Kenner, L. R., Swaney, D. L., Burlingame, A., Villén, J., Lim, W. A., Fraser, J. S., Frydman, J., & Krogan, N. J.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-07
- Volume
- 150
- Issue
- 2
- Pages
- 413-425
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2101876702
- Cited by
- 426
- References
- 10
- FWCI
- 15.96
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Beltrao, P., Albanèse, V., Kenner, L. R., Swaney, D. L., Burlingame, A., Villén, J., Lim, W. A., Fraser, J. S., Frydman, J., & Krogan, N. J. (2012). Systematic Functional Prioritization of Protein Posttranslational Modifications. Cell. https://doi.org/10.1016/j.cell.2012.05.036
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