Description of peptide bond planarity from high-resolution neutron crystallography
Neutron crystallography is a highly effective method for visualizing hydrogen atoms in proteins. In our recent study, we successfully determined the high-resolution (1.2 Å) neutron structure of high-potential iron-sulfur protein, refining the coordinates of some amide protons without any geometric r...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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The Biophysical Society of Japan
2023-09-01
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| Series: | Biophysics and Physicobiology |
| Subjects: | |
| Online Access: | https://doi.org/10.2142/biophysico.bppb-v20.0035 |
| _version_ | 1797674799173992448 |
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| author | Yuya Hanazono Yu Hirano Taro Tamada Kunio Miki |
| author_facet | Yuya Hanazono Yu Hirano Taro Tamada Kunio Miki |
| author_sort | Yuya Hanazono |
| collection | DOAJ |
| description | Neutron crystallography is a highly effective method for visualizing hydrogen atoms in proteins. In our recent study, we successfully determined the high-resolution (1.2 Å) neutron structure of high-potential iron-sulfur protein, refining the coordinates of some amide protons without any geometric restraints. Interestingly, we observed that amide protons are deviated from the peptide plane due to electrostatic interactions. Moreover, the difference in the position of the amide proton of Cys75 between reduced and oxidized states is possibly attributed to the electron storage capacity of the iron-sulfur cluster. Additionally, we have discussed about the rigidity of the iron-sulfur cluster based on the results of the hydrogen-deuterium exchange. Our research underscores the significance of neutron crystallography in protein structure elucidation, enriching our understanding of protein functions at an atomic resolution. |
| first_indexed | 2024-03-11T22:04:16Z |
| format | Article |
| id | doaj.art-dcdf95b6e8b34c63a23df8dc50beac0a |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-03-11T22:04:16Z |
| publishDate | 2023-09-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-dcdf95b6e8b34c63a23df8dc50beac0a2023-09-25T09:42:17ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792023-09-012010.2142/biophysico.bppb-v20.0035Description of peptide bond planarity from high-resolution neutron crystallographyYuya Hanazono0Yu Hirano1Taro Tamada2Kunio Miki3Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, JapanInstitute for Quantum Life Science, National Institutes for Quantum Science and Technology, Inage-ku, Chiba 263-8555, JapanInstitute for Quantum Life Science, National Institutes for Quantum Science and Technology, Inage-ku, Chiba 263-8555, JapanDepartment of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, JapanNeutron crystallography is a highly effective method for visualizing hydrogen atoms in proteins. In our recent study, we successfully determined the high-resolution (1.2 Å) neutron structure of high-potential iron-sulfur protein, refining the coordinates of some amide protons without any geometric restraints. Interestingly, we observed that amide protons are deviated from the peptide plane due to electrostatic interactions. Moreover, the difference in the position of the amide proton of Cys75 between reduced and oxidized states is possibly attributed to the electron storage capacity of the iron-sulfur cluster. Additionally, we have discussed about the rigidity of the iron-sulfur cluster based on the results of the hydrogen-deuterium exchange. Our research underscores the significance of neutron crystallography in protein structure elucidation, enriching our understanding of protein functions at an atomic resolution.https://doi.org/10.2142/biophysico.bppb-v20.0035high-resolution crystallographyiron-sulfur clusterh/d exchange |
| spellingShingle | Yuya Hanazono Yu Hirano Taro Tamada Kunio Miki Description of peptide bond planarity from high-resolution neutron crystallography Biophysics and Physicobiology high-resolution crystallography iron-sulfur cluster h/d exchange |
| title | Description of peptide bond planarity from high-resolution neutron crystallography |
| title_full | Description of peptide bond planarity from high-resolution neutron crystallography |
| title_fullStr | Description of peptide bond planarity from high-resolution neutron crystallography |
| title_full_unstemmed | Description of peptide bond planarity from high-resolution neutron crystallography |
| title_short | Description of peptide bond planarity from high-resolution neutron crystallography |
| title_sort | description of peptide bond planarity from high resolution neutron crystallography |
| topic | high-resolution crystallography iron-sulfur cluster h/d exchange |
| url | https://doi.org/10.2142/biophysico.bppb-v20.0035 |
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