Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin
Rational mutation of proteins based on their structural and dynamic characteristics is a useful strategy for amplifying specific fluctuations in proteins. Here, we show the effects of mutation on the conformational fluctuations and thermodynamic stability of ubiquitin. In particular, we focus on the...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2017-08-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/22/9/1414 |
| _version_ | 1818933972963426304 |
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| author | Soichiro Kitazawa Maho Yagi-Utsumi Koichi Kato Ryo Kitahara |
| author_facet | Soichiro Kitazawa Maho Yagi-Utsumi Koichi Kato Ryo Kitahara |
| author_sort | Soichiro Kitazawa |
| collection | DOAJ |
| description | Rational mutation of proteins based on their structural and dynamic characteristics is a useful strategy for amplifying specific fluctuations in proteins. Here, we show the effects of mutation on the conformational fluctuations and thermodynamic stability of ubiquitin. In particular, we focus on the salt bridge between K11 and E34 and the hydrogen bond between I36 and Q41, which are predicted to control the fluctuation between the basic folded state, N1, and the alternatively folded state, N2, of the protein, using high-pressure NMR spectroscopy. The E34A mutation, which disrupts the salt bridge, did not alter picosecond–to–nanosecond, microsecond–to–millisecond dynamic motions, and stability of the protein, while the Q41N mutation, which destabilizes the hydrogen bond, specifically amplified the N1–N2 conformational fluctuation and decreased stability. Based on the observed thermodynamic stabilities of the various conformational states, we showed that in the Q41N mutant, the N1 state is more significantly destabilized than the N2 state, resulting in an increase in the relative population of N2. Identifying the interactions controlling specific motions of a protein will facilitate molecular design to achieve functional dynamics beyond native state dynamics. |
| first_indexed | 2024-12-20T04:56:53Z |
| format | Article |
| id | doaj.art-1252beeb4b044c54a0846a426c9ee44d |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-20T04:56:53Z |
| publishDate | 2017-08-01 |
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| record_format | Article |
| series | Molecules |
| spelling | doaj.art-1252beeb4b044c54a0846a426c9ee44d2022-12-21T19:52:41ZengMDPI AGMolecules1420-30492017-08-01229141410.3390/molecules22091414molecules22091414Interactions Controlling the Slow Dynamic Conformational Motions of UbiquitinSoichiro Kitazawa0Maho Yagi-Utsumi1Koichi Kato2Ryo Kitahara3College of Pharmaceutical Sciences, Ritsumeikan University, Noji-higashi 1-1-1, Kusatsu 525-8577, JapanOkazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji-cho, Aza-higashiyama 5-1, Okazaki 444-8787, JapanOkazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji-cho, Aza-higashiyama 5-1, Okazaki 444-8787, JapanCollege of Pharmaceutical Sciences, Ritsumeikan University, Noji-higashi 1-1-1, Kusatsu 525-8577, JapanRational mutation of proteins based on their structural and dynamic characteristics is a useful strategy for amplifying specific fluctuations in proteins. Here, we show the effects of mutation on the conformational fluctuations and thermodynamic stability of ubiquitin. In particular, we focus on the salt bridge between K11 and E34 and the hydrogen bond between I36 and Q41, which are predicted to control the fluctuation between the basic folded state, N1, and the alternatively folded state, N2, of the protein, using high-pressure NMR spectroscopy. The E34A mutation, which disrupts the salt bridge, did not alter picosecond–to–nanosecond, microsecond–to–millisecond dynamic motions, and stability of the protein, while the Q41N mutation, which destabilizes the hydrogen bond, specifically amplified the N1–N2 conformational fluctuation and decreased stability. Based on the observed thermodynamic stabilities of the various conformational states, we showed that in the Q41N mutant, the N1 state is more significantly destabilized than the N2 state, resulting in an increase in the relative population of N2. Identifying the interactions controlling specific motions of a protein will facilitate molecular design to achieve functional dynamics beyond native state dynamics.https://www.mdpi.com/1420-3049/22/9/1414alternatively folded statehigh-pressure NMRubiquitin |
| spellingShingle | Soichiro Kitazawa Maho Yagi-Utsumi Koichi Kato Ryo Kitahara Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin Molecules alternatively folded state high-pressure NMR ubiquitin |
| title | Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin |
| title_full | Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin |
| title_fullStr | Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin |
| title_full_unstemmed | Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin |
| title_short | Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin |
| title_sort | interactions controlling the slow dynamic conformational motions of ubiquitin |
| topic | alternatively folded state high-pressure NMR ubiquitin |
| url | https://www.mdpi.com/1420-3049/22/9/1414 |
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