Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore
Direct observation of protein structural changes during ion transport in ion pumps provides valuable insights into the mechanism of ion transport. In this study, we examined structural changes in the light-driven sodium ion (Na+) pump rhodopsin KR2 on the sub-millisecond time scale, corresponding wi...
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| Format: | Article |
| Language: | English |
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The Biophysical Society of Japan
2023-03-01
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| Series: | Biophysics and Physicobiology |
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| Online Access: | https://doi.org/10.2142/biophysico.bppb-v20.s016 |
| _version_ | 1797797040446504960 |
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| author | Akihiro Otomo Misao Mizuno Keiichi Inoue Hideki Kandori Yasuhisa Mizutani |
| author_facet | Akihiro Otomo Misao Mizuno Keiichi Inoue Hideki Kandori Yasuhisa Mizutani |
| author_sort | Akihiro Otomo |
| collection | DOAJ |
| description | Direct observation of protein structural changes during ion transport in ion pumps provides valuable insights into the mechanism of ion transport. In this study, we examined structural changes in the light-driven sodium ion (Na+) pump rhodopsin KR2 on the sub-millisecond time scale, corresponding with the uptake and release of Na+. We compared the ion-pumping activities and transient absorption spectra of WT and the W215F mutant, in which the Trp215 residue located near the retinal chromophore on the cytoplasmic side was replaced with a Phe residue. Our findings indicated that atomic contacts between the bulky side chain of Trp215 and the C20 methyl group of the retinal chromophore promote relaxation of the retinal chromophore from the 13-cis to the all-trans form. Since Trp215 is conserved in other ion-pumping rhodopsins, the present results suggest that this residue commonly acts as a mechanical transducer. In addition, we measured time-resolved ultraviolet resonance Raman (UVRR) spectra to show that the environment around Trp215 becomes less hydrophobic at 1 ms after photoirradiation and recovers to the unphotolyzed state with a time constant of around 10 ms. These time scales correspond to Na+ uptake and release, suggesting evolution of a transient ion channel at the cytoplasmic side for Na+ uptake, consistent with the alternating-access model of ion pumps. The time-resolved UVRR technique has potential for application to other ion-pumping rhodopsins and could provide further insights into the mechanism of ion transport. |
| first_indexed | 2024-03-13T03:42:10Z |
| format | Article |
| id | doaj.art-105007c6684d4d85913488dc31d10f07 |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-03-13T03:42:10Z |
| publishDate | 2023-03-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-105007c6684d4d85913488dc31d10f072023-06-23T05:23:22ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792023-03-012010.2142/biophysico.bppb-v20.s016Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophoreAkihiro Otomo0Misao Mizuno1Keiichi Inoue2Hideki Kandori3Yasuhisa Mizutani4Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, JapanDepartment of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, JapanThe Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, JapanDepartment of Life Chemistry, Graduate School of Science, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, JapanDepartment of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, JapanDirect observation of protein structural changes during ion transport in ion pumps provides valuable insights into the mechanism of ion transport. In this study, we examined structural changes in the light-driven sodium ion (Na+) pump rhodopsin KR2 on the sub-millisecond time scale, corresponding with the uptake and release of Na+. We compared the ion-pumping activities and transient absorption spectra of WT and the W215F mutant, in which the Trp215 residue located near the retinal chromophore on the cytoplasmic side was replaced with a Phe residue. Our findings indicated that atomic contacts between the bulky side chain of Trp215 and the C20 methyl group of the retinal chromophore promote relaxation of the retinal chromophore from the 13-cis to the all-trans form. Since Trp215 is conserved in other ion-pumping rhodopsins, the present results suggest that this residue commonly acts as a mechanical transducer. In addition, we measured time-resolved ultraviolet resonance Raman (UVRR) spectra to show that the environment around Trp215 becomes less hydrophobic at 1 ms after photoirradiation and recovers to the unphotolyzed state with a time constant of around 10 ms. These time scales correspond to Na+ uptake and release, suggesting evolution of a transient ion channel at the cytoplasmic side for Na+ uptake, consistent with the alternating-access model of ion pumps. The time-resolved UVRR technique has potential for application to other ion-pumping rhodopsins and could provide further insights into the mechanism of ion transport.https://doi.org/10.2142/biophysico.bppb-v20.s016time-resolved resonance raman spectroscopymicrobial rhodopsinsodium ion pumpalternating-access model |
| spellingShingle | Akihiro Otomo Misao Mizuno Keiichi Inoue Hideki Kandori Yasuhisa Mizutani Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore Biophysics and Physicobiology time-resolved resonance raman spectroscopy microbial rhodopsin sodium ion pump alternating-access model |
| title | Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore |
| title_full | Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore |
| title_fullStr | Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore |
| title_full_unstemmed | Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore |
| title_short | Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore |
| title_sort | protein dynamics of a light driven na pump rhodopsin probed using a tryptophan residue near the retinal chromophore |
| topic | time-resolved resonance raman spectroscopy microbial rhodopsin sodium ion pump alternating-access model |
| url | https://doi.org/10.2142/biophysico.bppb-v20.s016 |
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