NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains
Ubiquitin (Ub) molecules can be enzymatically connected through a specific isopeptide linkage, thereby mediating various cellular processes by binding to Ub-interacting proteins through their hydrophobic surfaces. The Lys48-linked Ub chains, which serve as tags for proteasomal degradation, undergo c...
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MDPI AG
2020-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/15/5351 |
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| author | Methanee Hiranyakorn Saeko Yanaka Tadashi Satoh Thunchanok Wilasri Benchawan Jityuti Maho Yagi-Utsumi Koichi Kato |
| author_facet | Methanee Hiranyakorn Saeko Yanaka Tadashi Satoh Thunchanok Wilasri Benchawan Jityuti Maho Yagi-Utsumi Koichi Kato |
| author_sort | Methanee Hiranyakorn |
| collection | DOAJ |
| description | Ubiquitin (Ub) molecules can be enzymatically connected through a specific isopeptide linkage, thereby mediating various cellular processes by binding to Ub-interacting proteins through their hydrophobic surfaces. The Lys48-linked Ub chains, which serve as tags for proteasomal degradation, undergo conformational interconversions between open and closed states, in which the hydrophobic surfaces are exposed and shielded, respectively. Here, we provide a quantitative view of such dynamic processes of Lys48-linked triUb and tetraUb in solution. The native and cyclic forms of Ub chains are prepared with isotope labeling by in vitro enzymatic reactions. Our comparative NMR analyses using monomeric Ub and cyclic diUb as reference molecules enabled the quantification of populations of the open and closed states for each Ub unit of the native Ub chains. The data indicate that the most distal Ub unit in the Ub chains is the most apt to expose its hydrophobic surface, suggesting its preferential involvement in interactions with the Ub-recognizing proteins. We also demonstrate that a mutational modification of the distal end of the Ub chain can remotely affect the solvent exposure of the hydrophobic surfaces of the other Ub units, suggesting that Ub chains could be unique design frameworks for the creation of allosterically controllable multidomain proteins. |
| first_indexed | 2024-03-10T18:10:33Z |
| format | Article |
| id | doaj.art-e1663de5f4ed45048e046cb3e6565ab9 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T18:10:33Z |
| publishDate | 2020-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-e1663de5f4ed45048e046cb3e6565ab92023-11-20T08:11:15ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-07-012115535110.3390/ijms21155351NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin ChainsMethanee Hiranyakorn0Saeko Yanaka1Tadashi Satoh2Thunchanok Wilasri3Benchawan Jityuti4Maho Yagi-Utsumi5Koichi Kato6Department of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, JapanDepartment of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, JapanGraduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, JapanInstitute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, JapanInstitute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, JapanDepartment of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, JapanDepartment of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, JapanUbiquitin (Ub) molecules can be enzymatically connected through a specific isopeptide linkage, thereby mediating various cellular processes by binding to Ub-interacting proteins through their hydrophobic surfaces. The Lys48-linked Ub chains, which serve as tags for proteasomal degradation, undergo conformational interconversions between open and closed states, in which the hydrophobic surfaces are exposed and shielded, respectively. Here, we provide a quantitative view of such dynamic processes of Lys48-linked triUb and tetraUb in solution. The native and cyclic forms of Ub chains are prepared with isotope labeling by in vitro enzymatic reactions. Our comparative NMR analyses using monomeric Ub and cyclic diUb as reference molecules enabled the quantification of populations of the open and closed states for each Ub unit of the native Ub chains. The data indicate that the most distal Ub unit in the Ub chains is the most apt to expose its hydrophobic surface, suggesting its preferential involvement in interactions with the Ub-recognizing proteins. We also demonstrate that a mutational modification of the distal end of the Ub chain can remotely affect the solvent exposure of the hydrophobic surfaces of the other Ub units, suggesting that Ub chains could be unique design frameworks for the creation of allosterically controllable multidomain proteins.https://www.mdpi.com/1422-0067/21/15/5351Lys48-linked ubiquitin chainsNMRmultidomain proteincyclic protein |
| spellingShingle | Methanee Hiranyakorn Saeko Yanaka Tadashi Satoh Thunchanok Wilasri Benchawan Jityuti Maho Yagi-Utsumi Koichi Kato NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains International Journal of Molecular Sciences Lys48-linked ubiquitin chains NMR multidomain protein cyclic protein |
| title | NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains |
| title_full | NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains |
| title_fullStr | NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains |
| title_full_unstemmed | NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains |
| title_short | NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains |
| title_sort | nmr characterization of conformational interconversions of lys48 linked ubiquitin chains |
| topic | Lys48-linked ubiquitin chains NMR multidomain protein cyclic protein |
| url | https://www.mdpi.com/1422-0067/21/15/5351 |
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