Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center
Using the X-ray free-electron laser (XFEL) structures of the photosynthetic reaction center from Blastochloris viridis that show light-induced time-dependent structural changes (Dods et al., (2021) Nature 589, 310–314), we investigated time-dependent changes in the energetics of the electron-transfe...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2023-10-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/88955 |
| _version_ | 1827799193861750784 |
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| author | Gai Nishikawa Yu Sugo Keisuke Saito Hiroshi Ishikita |
| author_facet | Gai Nishikawa Yu Sugo Keisuke Saito Hiroshi Ishikita |
| author_sort | Gai Nishikawa |
| collection | DOAJ |
| description | Using the X-ray free-electron laser (XFEL) structures of the photosynthetic reaction center from Blastochloris viridis that show light-induced time-dependent structural changes (Dods et al., (2021) Nature 589, 310–314), we investigated time-dependent changes in the energetics of the electron-transfer pathway, considering the entire protein environment of the protein structures and titrating the redox-active sites in the presence of all fully equilibrated titratable residues. In the dark and charge separation intermediate structures, the calculated redox potential (Em) values for the accessory bacteriochlorophyll and bacteriopheophytin in the electron-transfer-active branch (BL and HL) are higher than those in the electron-transfer-inactive branch (BM and HM). However, the stabilization of the charge-separated [PLPM]•+HL•– state owing to protein reorganization is not clearly observed in the Em(HL) values in the charge-separated 5 ps ([PLPM]•+HL•– state) structure. Furthermore, the expected chlorin ring deformation upon formation of HL•– (saddling mode) is absent in the HL geometry of the original 5 ps structure. These findings suggest that there is no clear link between the time-dependent structural changes and the electron-transfer events in the XFEL structures. |
| first_indexed | 2024-03-11T19:48:05Z |
| format | Article |
| id | doaj.art-08c89a274fec4ebea7093aee6d659f9e |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-03-11T19:48:05Z |
| publishDate | 2023-10-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-08c89a274fec4ebea7093aee6d659f9e2023-10-05T14:27:38ZengeLife Sciences Publications LtdeLife2050-084X2023-10-011210.7554/eLife.88955Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction centerGai Nishikawa0Yu Sugo1Keisuke Saito2https://orcid.org/0000-0002-2293-9743Hiroshi Ishikita3https://orcid.org/0000-0002-5849-8150Department of Applied Chemistry, The University of Tokyo, Tokyo, JapanDepartment of Applied Chemistry, The University of Tokyo, Tokyo, JapanDepartment of Applied Chemistry, The University of Tokyo, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, JapanDepartment of Applied Chemistry, The University of Tokyo, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, JapanUsing the X-ray free-electron laser (XFEL) structures of the photosynthetic reaction center from Blastochloris viridis that show light-induced time-dependent structural changes (Dods et al., (2021) Nature 589, 310–314), we investigated time-dependent changes in the energetics of the electron-transfer pathway, considering the entire protein environment of the protein structures and titrating the redox-active sites in the presence of all fully equilibrated titratable residues. In the dark and charge separation intermediate structures, the calculated redox potential (Em) values for the accessory bacteriochlorophyll and bacteriopheophytin in the electron-transfer-active branch (BL and HL) are higher than those in the electron-transfer-inactive branch (BM and HM). However, the stabilization of the charge-separated [PLPM]•+HL•– state owing to protein reorganization is not clearly observed in the Em(HL) values in the charge-separated 5 ps ([PLPM]•+HL•– state) structure. Furthermore, the expected chlorin ring deformation upon formation of HL•– (saddling mode) is absent in the HL geometry of the original 5 ps structure. These findings suggest that there is no clear link between the time-dependent structural changes and the electron-transfer events in the XFEL structures.https://elifesciences.org/articles/88955X-ray free-electron laser structureelectron transfer dynamicstype II reaction centerredox potentialcharge separationchlorophyll |
| spellingShingle | Gai Nishikawa Yu Sugo Keisuke Saito Hiroshi Ishikita Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center eLife X-ray free-electron laser structure electron transfer dynamics type II reaction center redox potential charge separation chlorophyll |
| title | Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center |
| title_full | Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center |
| title_fullStr | Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center |
| title_full_unstemmed | Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center |
| title_short | Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center |
| title_sort | absence of electron transfer associated changes in the time dependent x ray free electron laser structures of the photosynthetic reaction center |
| topic | X-ray free-electron laser structure electron transfer dynamics type II reaction center redox potential charge separation chlorophyll |
| url | https://elifesciences.org/articles/88955 |
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