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Strongly Hydrogen-Bonded Schiff Base and Adjoining Polyene Twisting in the Retinal Chromophore of Schizorhodopsins

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Download Hi-Res ImageDownload to MS-PowerPointCite This:Biochemistry 2021, 60, 41, 3050-3057
    Article

    Strongly Hydrogen-Bonded Schiff Base and Adjoining Polyene Twisting in the Retinal Chromophore of Schizorhodopsins
    Click to copy article linkArticle link copied!

    • Tomomi Shionoya
      Tomomi Shionoya
      Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
      More by Tomomi Shionoya
    • Manish Singh
      Manish Singh
      Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
      More by Manish Singh
    • Misao Mizuno
      Misao Mizuno
      Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
      More by Misao Mizuno
      Orcidhttps://orcid.org/0000-0003-2206-1763
    • Hideki Kandori
      Hideki Kandori
      Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
      OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
      More by Hideki Kandori
      Orcidhttps://orcid.org/0000-0002-4922-1344
    • Yasuhisa Mizutani*
      Yasuhisa Mizutani
      Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
      *Email: [email protected]. Phone: +81-6-6850-5776.
      More by Yasuhisa Mizutani
      Orcidhttps://orcid.org/0000-0002-3754-5720
    Other Access OptionsSupporting Information (1)

    Biochemistry

    Cite this: Biochemistry 2021, 60, 41, 3050–3057
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    https://doi.org/10.1021/acs.biochem.1c00529
    Published October 3, 2021
    Copyright © 2021 American Chemical Society
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    Abstract

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    A transmembrane proton gradient is generated and maintained by proton pumps in a cell. Metagenomics studies have recently identified a new category of rhodopsin intermediates between type-1 rhodopsins and heliorhodopsins, named schizorhodopsins (SzRs). SzRs are light-driven inward proton pumps. Comprehensive resonance Raman measurements were conducted to characterize the structure of the retinal chromophore in the unphotolyzed state of four SzRs. The spectra of all four SzRs show that the retinal chromophore is in the all-trans and 15-anti configuration and that the Schiff base is protonated. The polyene chain is planar in the center of the retinal chromophore and is twisted in the vicinity of the protonated Schiff base. The protonated Schiff base in the SzRs forms a stronger hydrogen bond than that in outward proton-pumping rhodopsins. We determined that the hydrogen-bonding partner of the protonated Schiff base is not a water molecule but an amino acid residue, presumably an Asp residue in helix G. The present observations provide valuable insights into the inward proton-pumping mechanism of SzRs.

    Copyright © 2021 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.biochem.1c00529.

    • Absorption spectra of SzRs, RR spectra of SzRs in D2O buffer probed at 532 nm, enlarged views of RR spectra of SzRs in the C═N stretching region (1560–1680 cm–1), RR spectra of SzRs in a mixed buffer (H2O/D2O = 1:1) probed at 532 nm, and plot of the C═C stretching frequencies against the absorption maximum wavelengths of the retinal chromophore (PDF)

    Accession Codes

    SzR1, GenBank accession number: TFG18381. SzR3, GenBank accession number: TFF95899. SzR4, GenBank accession number: TFG21677.1.

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    Cited By

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    This article is cited by 11 publications.

    1. Taiki Nakamura, Yuka Shinozaki, Akihiro Otomo, Taito Urui, Misao Mizuno, Rei Abe-Yoshizumi, Manami Hashimoto, Keiichi Kojima, Yuki Sudo, Hideki Kandori, Yasuhisa Mizutani. Unusual Vibrational Coupling of the Schiff Base in the Retinal Chromophore of Sodium Ion-Pumping Rhodopsins. The Journal of Physical Chemistry B 2024, 128 (32) , 7813-7821. https://doi.org/10.1021/acs.jpcb.4c04466
    2. Taito Urui, Tomomi Shionoya, Misao Mizuno, Keiichi Inoue, Hideki Kandori, Yasuhisa Mizutani. Chromophore–Protein Interactions Affecting the Polyene Twist and π–π* Energy Gap of the Retinal Chromophore in Schizorhodopsins. The Journal of Physical Chemistry B 2024, 128 (10) , 2389-2397. https://doi.org/10.1021/acs.jpcb.3c08465
    3. Taito Urui, Kouhei Hayashi, Misao Mizuno, Keiichi Inoue, Hideki Kandori, Yasuhisa Mizutani. Cis–Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping. The Journal of Physical Chemistry B 2024, 128 (3) , 744-754. https://doi.org/10.1021/acs.jpcb.3c07510
    4. Zixuan Li, Misao Mizuno, Tomo Ejiri, Shigehiko Hayashi, Hideki Kandori, Yasuhisa Mizutani. Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins. The Journal of Physical Chemistry B 2023, 127 (46) , 9873-9886. https://doi.org/10.1021/acs.jpcb.3c02146
    5. Maryam Saliminasab, Yoichi Yamazaki, Alyssa Palmateer, Andrew Harris, Luiz Schubert, Pit Langner, Joachim Heberle, Ana-Nicoleta Bondar, Leonid S. Brown. A Proteorhodopsin-Related Photosensor Expands the Repertoire of Structural Motifs Employed by Sensory Rhodopsins. The Journal of Physical Chemistry B 2023, 127 (37) , 7872-7886. https://doi.org/10.1021/acs.jpcb.3c04032
    6. Chun-Fu Chang, Masae Konno, Keiichi Inoue, Tahei Tahara. Effects of the Unique Chromophore–Protein Interactions on the Primary Photoreaction of Schizorhodopsin. The Journal of Physical Chemistry Letters 2023, 14 (31) , 7083-7091. https://doi.org/10.1021/acs.jpclett.3c01133
    7. Keisei Shibata, Kazumasa Oda, Tomohiro Nishizawa, Yuji Hazama, Ryohei Ono, Shunki Takaramoto, Reza Bagherzadeh, Hiromu Yawo, Osamu Nureki, Keiichi Inoue, Hidefumi Akiyama. Twisting and Protonation of Retinal Chromophore Regulate Channel Gating of Channelrhodopsin C1C2. Journal of the American Chemical Society 2023, 145 (19) , 10779-10789. https://doi.org/10.1021/jacs.3c01879
    8. Taito Urui, Ishita Das, Misao Mizuno, Mordechai Sheves, Yasuhisa Mizutani. Origin of a Double-Band Feature in the Ethylenic C═C Stretching Modes of the Retinal Chromophore in Heliorhodopsins. The Journal of Physical Chemistry B 2022, 126 (43) , 8680-8688. https://doi.org/10.1021/acs.jpcb.2c04883
    9. Kouhei Hayashi, Misao Mizuno, Hideki Kandori, Yasuhisa Mizutani. Cis – Trans Reisomerization Precedes Reprotonation of the Retinal Chromophore in the Photocycle of Schizorhodopsin 4. Angewandte Chemie 2022, 134 (33) https://doi.org/10.1002/ange.202203149
    10. Kouhei Hayashi, Misao Mizuno, Hideki Kandori, Yasuhisa Mizutani. Cis – Trans Reisomerization Precedes Reprotonation of the Retinal Chromophore in the Photocycle of Schizorhodopsin 4. Angewandte Chemie International Edition 2022, 61 (33) https://doi.org/10.1002/anie.202203149
    11. Leonid S. Brown. Light-driven proton transfers and proton transport by microbial rhodopsins – A biophysical perspective. Biochimica et Biophysica Acta (BBA) - Biomembranes 2022, 1864 (5) , 183867. https://doi.org/10.1016/j.bbamem.2022.183867
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    Biochemistry

    Cite this: Biochemistry 2021, 60, 41, 3050–3057
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.biochem.1c00529
    Published October 3, 2021
    Copyright © 2021 American Chemical Society
    Request reuse permissions

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