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Non-degradative Ubiquitination of Protein Kinases
Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation. In contrast to other common post-translational modifications, such as phosphorylation, little is known about how non-degradative ubiquitination modulates protein s...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890936/ https://www.ncbi.nlm.nih.gov/pubmed/27253329 http://dx.doi.org/10.1371/journal.pcbi.1004898 |
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author | Ball, K. Aurelia Johnson, Jeffrey R. Lewinski, Mary K. Guatelli, John Verschueren, Erik Krogan, Nevan J. Jacobson, Matthew P. |
author_facet | Ball, K. Aurelia Johnson, Jeffrey R. Lewinski, Mary K. Guatelli, John Verschueren, Erik Krogan, Nevan J. Jacobson, Matthew P. |
author_sort | Ball, K. Aurelia |
collection | PubMed |
description | Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation. In contrast to other common post-translational modifications, such as phosphorylation, little is known about how non-degradative ubiquitination modulates protein structure, dynamics, and function. Due to the wealth of knowledge concerning protein kinase structure and regulation, we examined kinase ubiquitination using ubiquitin remnant immunoaffinity enrichment and quantitative mass spectrometry to identify ubiquitinated kinases and the sites of ubiquitination in Jurkat and HEK293 cells. We find that, unlike phosphorylation, ubiquitination most commonly occurs in structured domains, and on the kinase domain, ubiquitination is concentrated in regions known to be important for regulating activity. We hypothesized that ubiquitination, like other post-translational modifications, may alter the conformational equilibrium of the modified protein. We chose one human kinase, ZAP-70, to simulate using molecular dynamics with and without a monoubiquitin modification. In Jurkat cells, ZAP-70 is ubiquitinated at several sites that are not sensitive to proteasome inhibition and thus may have other regulatory roles. Our simulations show that ubiquitination influences the conformational ensemble of ZAP-70 in a site-dependent manner. When monoubiquitinated at K377, near the C-helix, the active conformation of the ZAP-70 C-helix is disrupted. In contrast, when monoubiquitinated at K476, near the kinase hinge region, an active-like ZAP-70 C-helix conformation is stabilized. These results lead to testable hypotheses that ubiquitination directly modulates kinase activity, and that ubiquitination is likely to alter structure, dynamics, and function in other protein classes as well. |
format | Online Article Text |
id | pubmed-4890936 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-48909362016-06-10 Non-degradative Ubiquitination of Protein Kinases Ball, K. Aurelia Johnson, Jeffrey R. Lewinski, Mary K. Guatelli, John Verschueren, Erik Krogan, Nevan J. Jacobson, Matthew P. PLoS Comput Biol Research Article Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation. In contrast to other common post-translational modifications, such as phosphorylation, little is known about how non-degradative ubiquitination modulates protein structure, dynamics, and function. Due to the wealth of knowledge concerning protein kinase structure and regulation, we examined kinase ubiquitination using ubiquitin remnant immunoaffinity enrichment and quantitative mass spectrometry to identify ubiquitinated kinases and the sites of ubiquitination in Jurkat and HEK293 cells. We find that, unlike phosphorylation, ubiquitination most commonly occurs in structured domains, and on the kinase domain, ubiquitination is concentrated in regions known to be important for regulating activity. We hypothesized that ubiquitination, like other post-translational modifications, may alter the conformational equilibrium of the modified protein. We chose one human kinase, ZAP-70, to simulate using molecular dynamics with and without a monoubiquitin modification. In Jurkat cells, ZAP-70 is ubiquitinated at several sites that are not sensitive to proteasome inhibition and thus may have other regulatory roles. Our simulations show that ubiquitination influences the conformational ensemble of ZAP-70 in a site-dependent manner. When monoubiquitinated at K377, near the C-helix, the active conformation of the ZAP-70 C-helix is disrupted. In contrast, when monoubiquitinated at K476, near the kinase hinge region, an active-like ZAP-70 C-helix conformation is stabilized. These results lead to testable hypotheses that ubiquitination directly modulates kinase activity, and that ubiquitination is likely to alter structure, dynamics, and function in other protein classes as well. Public Library of Science 2016-06-02 /pmc/articles/PMC4890936/ /pubmed/27253329 http://dx.doi.org/10.1371/journal.pcbi.1004898 Text en © 2016 Ball et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Ball, K. Aurelia Johnson, Jeffrey R. Lewinski, Mary K. Guatelli, John Verschueren, Erik Krogan, Nevan J. Jacobson, Matthew P. Non-degradative Ubiquitination of Protein Kinases |
title | Non-degradative Ubiquitination of Protein Kinases |
title_full | Non-degradative Ubiquitination of Protein Kinases |
title_fullStr | Non-degradative Ubiquitination of Protein Kinases |
title_full_unstemmed | Non-degradative Ubiquitination of Protein Kinases |
title_short | Non-degradative Ubiquitination of Protein Kinases |
title_sort | non-degradative ubiquitination of protein kinases |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890936/ https://www.ncbi.nlm.nih.gov/pubmed/27253329 http://dx.doi.org/10.1371/journal.pcbi.1004898 |
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