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  1. Article ; Online: Near-Infrared Excited Raman Optical Activity as a Tool to Uncover Active Sites of Photoreceptor Proteins.

    Fujisawa, Tomotsumi / Unno, Masashi

    The journal of physical chemistry. B

    2024  Volume 128, Issue 10, Page(s) 2228–2235

    Abstract: Raman optical activity (ROA) is a chiral sensitive technique to measure the difference in Raman scattering intensity between right and left circularly polarized light. The method has been applied to the study of biological molecules such as proteins, and ...

    Abstract Raman optical activity (ROA) is a chiral sensitive technique to measure the difference in Raman scattering intensity between right and left circularly polarized light. The method has been applied to the study of biological molecules such as proteins, and it is now recognized as a powerful tool for investigating biomolecular structures. We have expanded the capability of this chiroptical technique to colored molecules, such as photoreceptor proteins, by using a near-infrared excitation. A photoreceptor protein contains a light-absorbing chromophore as an active site, and the precise determination of its structure is vital for comprehending the protein's function at the atomic level. In a photoreceptor protein, the protein environment can distort an achiral chromophore into a chiral conformation. ROA spectroscopy offers detailed structural information about the chromophore under physiological conditions. Here we explore recent progress in near-infrared ROA spectroscopy and its application to biological systems.
    MeSH term(s) Optical Rotation ; Catalytic Domain ; Proteins/chemistry ; Spectrum Analysis, Raman/methods
    Chemical Substances Proteins
    Language English
    Publishing date 2024-03-05
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.4c00094
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Configurational Changes of Retinal Schiff Base during Membrane Na

    Fujisawa, Tomotsumi / Kinoue, Kouta / Seike, Ryouhei / Kikukawa, Takashi / Unno, Masashi

    The journal of physical chemistry letters

    2024  Volume 15, Issue 7, Page(s) 1993–1998

    Abstract: Microbial rhodopsins are photoreceptors containing the retinal Schiff base chromophore and are ubiquitous among microorganisms. The Schiff base configuration of the chromophore, 15- ...

    Abstract Microbial rhodopsins are photoreceptors containing the retinal Schiff base chromophore and are ubiquitous among microorganisms. The Schiff base configuration of the chromophore, 15-
    MeSH term(s) Rhodopsin/chemistry ; Schiff Bases/chemistry ; Ions ; Ion Transport ; Rhodopsins, Microbial ; Sodium/chemistry
    Chemical Substances Rhodopsin (9009-81-8) ; Schiff Bases ; Ions ; Rhodopsins, Microbial ; Sodium (9NEZ333N27)
    Language English
    Publishing date 2024-02-13
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c03435
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Molecular Vibrations in Chiral Europium Complexes Revealed by Near-Infrared Raman Optical Activity.

    Wu, Tao / Bouř, Petr / Fujisawa, Tomotsumi / Unno, Masashi

    Advanced science (Weinheim, Baden-Wurttemberg, Germany)

    2023  Volume 11, Issue 1, Page(s) e2305521

    Abstract: Raman optical activity (ROA) is commonly measured with green light (532 nm) excitation. At this wavelength, however, Raman scattering of europium complexes is masked by circularly polarized luminescence (CPL). This can be avoided using near-infrared ( ... ...

    Abstract Raman optical activity (ROA) is commonly measured with green light (532 nm) excitation. At this wavelength, however, Raman scattering of europium complexes is masked by circularly polarized luminescence (CPL). This can be avoided using near-infrared (near-IR, 785 nm) laser excitation, as demonstrated here by Raman and ROA spectra of three chiral europium complexes derived from camphor. Since luminescence is strongly suppressed, many vibrational bands can be detected. They carry a wealth of structural information about the ligand and the metal core, and can be interpreted based on density functional theory (DFT) simulations of the spectra. For example, jointly with ROA experimental data, the simulations make it possible to determine absolute configuration of chiral lanthanide compounds in solution.
    Language English
    Publishing date 2023-11-20
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2808093-2
    ISSN 2198-3844 ; 2198-3844
    ISSN (online) 2198-3844
    ISSN 2198-3844
    DOI 10.1002/advs.202305521
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II.

    Nishikawa, Kouhei / Kuroiwa, Ryosuke / Tamogami, Jun / Unno, Masashi / Fujisawa, Tomotsumi

    The journal of physical chemistry. B

    2023  Volume 127, Issue 33, Page(s) 7244–7250

    Abstract: Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal chromophore in sensory rhodopsin II (SRII), which is a blue-green light sensor of microbes. The ROA spectrum consisted of the negative vibrational bands of the ... ...

    Abstract Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal chromophore in sensory rhodopsin II (SRII), which is a blue-green light sensor of microbes. The ROA spectrum consisted of the negative vibrational bands of the chromophore, whose relative intensities are similar to those of the parent Raman spectrum. This spectral feature was explained by the left-handed helical twist of the retinal chromophore on the basis of quantum chemical calculations. On the other hand, we found that the chromophore conformation based on the crystal structures of SRII has a right-handed helical twist, which does not agree with the observation. This specific result suggests that the consistency with chiro-optical properties can be a key criterion for the accurate prediction and/or evaluation of chromophore conformation in retinal-binding proteins.
    MeSH term(s) Sensory Rhodopsins/chemistry ; Optical Rotation ; Retina ; Spectrum Analysis, Raman ; Rhodopsin/chemistry
    Chemical Substances Sensory Rhodopsins ; Rhodopsin (9009-81-8)
    Language English
    Publishing date 2023-08-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c02391
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Reisomerization of retinal represents a molecular switch mediating Na

    Fujisawa, Tomotsumi / Kinoue, Kouta / Seike, Ryouhei / Kikukawa, Takashi / Unno, Masashi

    The Journal of biological chemistry

    2022  Volume 298, Issue 9, Page(s) 102366

    Abstract: Sodium-pumping rhodopsins (NaRs) are membrane transporters that utilize light energy to pump ... ...

    Abstract Sodium-pumping rhodopsins (NaRs) are membrane transporters that utilize light energy to pump Na
    MeSH term(s) Bacteriorhodopsins/metabolism ; Bacteroidetes/metabolism ; Ion Transport ; Light ; Schiff Bases ; Sodium/metabolism ; Spectrum Analysis, Raman
    Chemical Substances Schiff Bases ; Bacteriorhodopsins (53026-44-1) ; Sodium (9NEZ333N27)
    Language English
    Publishing date 2022-08-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2022.102366
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Conformational Analysis of a Retinal Schiff Base Chromophore in Proteorhodopsin by Raman Optical Activity.

    Fujisawa, Tomotsumi / Nishikawa, Kouhei / Tamogami, Jun / Unno, Masashi

    The journal of physical chemistry letters

    2021  Volume 12, Issue 39, Page(s) 9564–9568

    Abstract: Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal Schiff base chromophore in green-light-absorbing proteorhodopsin, which is a globally distributed light-driven proton pump of aquatic bacteria. The ROA spectrum ... ...

    Abstract Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal Schiff base chromophore in green-light-absorbing proteorhodopsin, which is a globally distributed light-driven proton pump of aquatic bacteria. The ROA spectrum consisted mostly of the negative vibrational bands of the chromophore, while the hydrogen out-of-plane mode (at 960 cm
    Language English
    Publishing date 2021-09-28
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.1c02552
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  7. Article ; Online: Why Does One Measure Resonance Raman Optical Activity? A Unique Case of Measurements under Strong Resonance versus Far-from-Resonance Conditions.

    Machalska, Ewa / Halat, Monika / Tani, Takumi / Fujisawa, Tomotsumi / Unno, Masashi / Kudelski, Andrzej / Baranska, Malgorzata / Zając, Grzegorz

    The journal of physical chemistry letters

    2024  Volume 15, Issue 18, Page(s) 4913–4919

    Abstract: Raman optical activity (ROA) spectroscopy exhibits significant potential in the study of (bio)molecules as it encodes information on their molecular structure, chirality, and conformations. Furthermore, the method reveals details on excited electronic ... ...

    Abstract Raman optical activity (ROA) spectroscopy exhibits significant potential in the study of (bio)molecules as it encodes information on their molecular structure, chirality, and conformations. Furthermore, the method reveals details on excited electronic states when applied under resonance conditions. Here, we present a combined study of the far from resonance (FFR)-ROA and resonance ROA (RROA) of a single relatively small molecular system. Notably, this study is the first to employ the density functional theory (DFT) analysis of both FFR-ROA and RROA spectra. This is illustrated for cobalamin derivatives using near-infrared and visible light excitation. Although the commonly observed monosignate RROA spectra lose additional information visible in bisignate nonresonance ROA spectra, the RROA technique acts as a complement to nonresonance ROA spectroscopy. In particular, the combination of these methods integrated with DFT calculations can reveal a complete spectral picture of the structural and conformational differences between tested compounds.
    Language English
    Publishing date 2024-04-29
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.4c00270
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  8. Article ; Online: Structure and Heterogeneity of Retinal Chromophore in Chloride Pump Rhodopsins Revealed by Raman Optical Activity.

    Ohya, Masaiku / Kikukawa, Takashi / Matsuo, Junpei / Tsukamoto, Takashi / Nagaura, Ryota / Fujisawa, Tomotsumi / Unno, Masashi

    The journal of physical chemistry. B

    2023  Volume 127, Issue 21, Page(s) 4775–4782

    Abstract: Chloride transport by microbial rhodopsins is actively being researched to understand how light energy is converted to drive ion pumping across cell membranes. Chloride pumps have been identified in archaea and eubacteria, and there are similarities and ... ...

    Abstract Chloride transport by microbial rhodopsins is actively being researched to understand how light energy is converted to drive ion pumping across cell membranes. Chloride pumps have been identified in archaea and eubacteria, and there are similarities and differences in the active site structures between these groups. Thus, it has not been clarified whether a common mechanism underlies the ion pump processes for all chloride-pumping rhodopsins. Here, we applied Raman optical activity (ROA) spectroscopy to two chloride pumps,
    MeSH term(s) Rhodopsin/chemistry ; Chlorides/chemistry ; Schiff Bases ; Optical Rotation ; Rhodopsins, Microbial/metabolism ; Ion Pumps ; Light
    Chemical Substances Rhodopsin (9009-81-8) ; Chlorides ; Schiff Bases ; Rhodopsins, Microbial ; Ion Pumps
    Language English
    Publishing date 2023-05-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c01801
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Spectroscopic Validation of Crystallographic Structures of a Protein Active Site by Chiroptical Spectroscopy.

    Fujisawa, Tomotsumi / Shingae, Takahito / Ren, Jie / Haraguchi, Shojiro / Hanamoto, Takeshi / Hoff, Wouter D / Unno, Masashi

    The journal of physical chemistry letters

    2023  Volume 14, Issue 41, Page(s) 9304–9309

    Abstract: Out-of-plane distortions of a cofactor molecule in a protein active site are functionally important, and in photoreceptors, it has been proposed that they are crucial for spectral tuning and energy storage in photocycle intermediates. However, these ... ...

    Abstract Out-of-plane distortions of a cofactor molecule in a protein active site are functionally important, and in photoreceptors, it has been proposed that they are crucial for spectral tuning and energy storage in photocycle intermediates. However, these subtle structural features are often beyond the grasp of structural biology. This issue is strikingly exemplified by photoactive yellow protein: its 14 independently determined crystal structures exhibit considerable differences in the dihedral angles defining the chromophore geometry, even though most of these are at excellent resolution. Here we developed a strategy to verify cofactor distortions in crystal structures by using quantum chemical calculations and chiroptical spectroscopy, particularly Raman optical activity and electronic circular dichroism spectroscopies. Based on this approach, we identify seven crystal structures with the chromophore geometries inconsistent with the experimentally observed data. The strategy implemented here promises to be widely applicable to uncovering cofactor distortions at active sites and to studies of reaction intermediates.
    MeSH term(s) Catalytic Domain ; Spectrum Analysis, Raman/methods ; Bacterial Proteins/chemistry ; Crystallography ; Spectrophotometry, Ultraviolet ; Photoreceptors, Microbial/chemistry
    Chemical Substances Bacterial Proteins ; Photoreceptors, Microbial
    Language English
    Publishing date 2023-10-10
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c01954
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Raman Spectroscopy of an Atypical C15-E,syn Bilin Chromophore in Cyanobacteriochrome RcaE

    Okuda, Yuji / Miyoshi, Risako / Kamo, Takanari / Fujisawa, Tomotsumi / Nagae, Takayuki / Mishima, Masaki / Eki, Toshihiko / Hirose, Yuu / Unno, Masashi

    Journal of physical chemistry. 2022 Jan. 25, v. 126, no. 4

    2022  

    Abstract: Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts ... ...

    Abstract Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts between a green-absorbing dark state and red-absorbing photoproduct (Pr). Our recent crystallographic study showed that the phycocyanobilin (PCB) chromophore of RcaE adopts a unique C15-E,syn configuration in the Pr state, unlike the typical C15-E,anti configuration for the phytochromes and other CBCRs. Here, we measured Raman spectra of the Pr state of RcaE with 1064 nm excitation and explored the structure of PCB and its interacting residues under physiologically relevant aqueous conditions. We also performed measurements of RcaE in D₂O as well as the sample reconstituted with the PCB labeled with ¹⁵N or with both ¹³C and ¹⁵N. The observed Raman spectra were analyzed by quantum mechanics/molecular mechanics (QM/MM) calculations together with molecular dynamics simulations. The Raman spectra and their isotope effects were well-reproduced by the simulated spectra of fully protonated PCB with the C15-E,syn configuration and allowed us to assign most of the observed bands. The present vibrational analysis of the all syn bilin chromophore using the QM/MM method will advance future studies on CBCRs and the related proteins by vibrational spectroscopy.
    Keywords Raman spectroscopy ; molecular dynamics ; phytochrome ; quantum mechanics
    Language English
    Dates of publication 2022-0125
    Size p. 813-821.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021/acs.jpcb.1c09652
    Database NAL-Catalogue (AGRICOLA)

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