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  1. Article ; Online: The preferential transport of NO

    Ohki, Yuya / Shinone, Tsukasa / Inoko, Sayo / Sudo, Miu / Demura, Makoto / Kikukawa, Takashi / Tsukamoto, Takashi

    The Journal of biological chemistry

    2023  Volume 299, Issue 11, Page(s) 105305

    Abstract: Previous research of anion channelrhodopsins (ACRs) has been performed using cytoplasmic domain (CPD)-deleted constructs and therefore have overlooked the native functions of full-length ACRs and the potential functional role(s) of the CPD. In this study, ...

    Abstract Previous research of anion channelrhodopsins (ACRs) has been performed using cytoplasmic domain (CPD)-deleted constructs and therefore have overlooked the native functions of full-length ACRs and the potential functional role(s) of the CPD. In this study, we used the recombinant expression of full-length Guillardia theta ACR1 (GtACR1_full) for pH measurements in Pichia pastoris cell suspensions as an indirect method to assess its anion transport activity and for absorption spectroscopy and flash photolysis characterization of the purified protein. The results show that the CPD, which was predicted to be intrinsically disordered and possibly phosphorylated, enhanced NO
    MeSH term(s) Anions/metabolism ; Channelrhodopsins/metabolism ; Cryptophyta/metabolism ; Ion Transport ; Nitrates/metabolism
    Chemical Substances Anions ; Channelrhodopsins ; Nitrates
    Language English
    Publishing date 2023-09-29
    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.2023.105305
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  2. Article ; Online: Real-time identification of two substrate-binding intermediates for the light-driven sodium pump rhodopsin.

    Kato, Tomoya / Tsukamoto, Takashi / Demura, Makoto / Kikukawa, Takashi

    The Journal of biological chemistry

    2021  Volume 296, Page(s) 100792

    Abstract: Membrane transport proteins undergo critical conformational changes during substrate uptake and release, as the substrate-binding site is believed to switch its accessibility from one side of the membrane to the other. Thus, at least two substrate- ... ...

    Abstract Membrane transport proteins undergo critical conformational changes during substrate uptake and release, as the substrate-binding site is believed to switch its accessibility from one side of the membrane to the other. Thus, at least two substrate-binding intermediates should appear during the process, that is, after uptake and before the release of the substrate. However, this view has not been verified for most transporters because of the difficulty in detecting short-lived intermediates. Here, we report real-time identification of these intermediates for the light-driven outward current-generating Na
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Bacteroidetes/chemistry ; Bacteroidetes/metabolism ; Light ; Rhodopsin/chemistry ; Rhodopsin/metabolism ; Sodium/chemistry ; Sodium/metabolism
    Chemical Substances Bacterial Proteins ; Rhodopsin (9009-81-8) ; Sodium (9NEZ333N27)
    Language English
    Publishing date 2021-05-18
    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.2021.100792
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  3. Article ; Online: Replaceability of Schiff base proton donors in light-driven proton pump rhodopsins.

    Sasaki, Syogo / Tamogami, Jun / Nishiya, Koki / Demura, Makoto / Kikukawa, Takashi

    The Journal of biological chemistry

    2021  Volume 297, Issue 3, Page(s) 101013

    Abstract: ... Many ... ...

    Abstract Many H
    MeSH term(s) Amino Acid Substitution ; Light ; Protein Conformation ; Protons ; Reproducibility of Results ; Rhodopsin/chemistry ; Schiff Bases/chemistry
    Chemical Substances Protons ; Schiff Bases ; Rhodopsin (9009-81-8)
    Language English
    Publishing date 2021-07-28
    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.2021.101013
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  4. Article ; Online: Mutations conferring SO

    Doi, Yuhei / Watanabe, Jo / Nii, Ryota / Tsukamoto, Takashi / Demura, Makoto / Sudo, Yuki / Kikukawa, Takashi

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 16422

    Abstract: Membrane transport proteins can be divided into two types: those that bind substrates in a resting state and those that do not. In this study, we demonstrate that these types can be converted by mutations through a study of two cyanobacterial anion- ... ...

    Abstract Membrane transport proteins can be divided into two types: those that bind substrates in a resting state and those that do not. In this study, we demonstrate that these types can be converted by mutations through a study of two cyanobacterial anion-pumping rhodopsins, Mastigocladopsis repens halorhodopsin (MrHR) and Synechocystis halorhodopsin (SyHR). Anion pump rhodopsins, including MrHR and SyHR, initially bind substrate anions to the protein center and transport them upon illumination. MrHR transports only smaller halide ions, Cl
    MeSH term(s) Anion Transport Proteins/genetics ; Anions/metabolism ; Chlorides/metabolism ; Cyanobacteria ; Halorhodopsins/metabolism ; Light ; Mutation ; Rhodopsin/metabolism ; Synechocystis/genetics ; Synechocystis/metabolism
    Chemical Substances Anion Transport Proteins ; Anions ; Chlorides ; Halorhodopsins ; Rhodopsin (9009-81-8)
    Language English
    Publishing date 2022-09-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-20784-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Direct Detection of the Substrate Uptake and Release Reactions of the Light-Driven Sodium-Pump Rhodopsin.

    Murabe, Keisuke / Tsukamoto, Takashi / Aizawa, Tomoyasu / Demura, Makoto / Kikukawa, Takashi

    Journal of the American Chemical Society

    2020  Volume 142, Issue 37, Page(s) 16023–16030

    Abstract: For membrane transporters, substrate uptake and release reactions are major events during their transport cycles. Despite the functional importance of these events, it is difficult to identify their relevant structural intermediates because of the ... ...

    Abstract For membrane transporters, substrate uptake and release reactions are major events during their transport cycles. Despite the functional importance of these events, it is difficult to identify their relevant structural intermediates because of the requirements of the experimental methods, which are to detect the timing of the formation and decay of intermediates and to detect the timing of substrate uptake and release. We report successfully achieving this for the light-driven Na
    Language English
    Publishing date 2020-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.0c07264
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  6. Article ; Online: Preference of Proteomonas sulcata anion channelrhodopsin for NO

    Kikuchi, Chihiro / Kurane, Hina / Watanabe, Takuma / Demura, Makoto / Kikukawa, Takashi / Tsukamoto, Takashi

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 7908

    Abstract: Ion channel proteins are physiologically important molecules in living organisms. Their molecular functions have been investigated using electrophysiological methods, which enable quantitative, precise and advanced measurements and thus require complex ... ...

    Abstract Ion channel proteins are physiologically important molecules in living organisms. Their molecular functions have been investigated using electrophysiological methods, which enable quantitative, precise and advanced measurements and thus require complex instruments and experienced operators. For simpler and easier measurements, we measured the anion transport activity of light-gated anion channelrhodopsins (ACRs) using a pH electrode method, which has already been established for ion pump rhodopsins. Using that method, we successfully measured the anion transport activity and its dependence on the wavelength of light, i.e. its action spectra, and on the anion species, i.e. its selectivity or preference, of several ACRs expressed in yeast cells. In addition, we identified the strong anion transport activity and the preference for NO
    MeSH term(s) Anions ; Biological Transport ; Channelrhodopsins/metabolism ; Cryptophyta/metabolism ; Electrodes ; Hydrogen-Ion Concentration ; Mutation/genetics ; Nitrates/metabolism ; Pichia/metabolism
    Chemical Substances Anions ; Channelrhodopsins ; Nitrates
    Language English
    Publishing date 2021-04-12
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-86812-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Direct Detection of the Substrate Uptake and Release Reactions of the Light-Driven Sodium-Pump Rhodopsin

    Murabe, Keisuke / Tsukamoto, Takashi / Aizawa, Tomoyasu / Demura, Makoto / Kikukawa, Takashi

    Journal of the American Chemical Society. 2020 Aug. 26, v. 142, no. 37

    2020  

    Abstract: For membrane transporters, substrate uptake and release reactions are major events during their transport cycles. Despite the functional importance of these events, it is difficult to identify their relevant structural intermediates because of the ... ...

    Abstract For membrane transporters, substrate uptake and release reactions are major events during their transport cycles. Despite the functional importance of these events, it is difficult to identify their relevant structural intermediates because of the requirements of the experimental methods, which are to detect the timing of the formation and decay of intermediates and to detect the timing of substrate uptake and release. We report successfully achieving this for the light-driven Na⁺ pump rhodopsin (NaR). Here, a Na⁺-selective membrane, which consists of polyvinyl chloride and a Na⁺ ionophore, was employed to detect Na⁺ uptake and release. When one side of the membrane was covered by the lipid-reconstituted NaR, continuous illumination induced an increase in membrane potential, which reflected Na⁺ uptake by the photolyzed NaR. Via use of nanosecond laser pulses, two kinds of data were obtained during a single transport cycle: one was the flash-induced absorbance change in NaR to detect the formation and decay of structural intermediates, and the other was the flash-induced change in membrane potential, which reflects the transient Na⁺ uptake and release reactions. Their comparison clearly indicated that Na⁺ is captured and released during the formation and decay of the O intermediate, the red-shifted intermediate that appears in the latter half of the transport cycle.
    Keywords absorbance ; lighting ; membrane potential ; poly(vinyl chloride) ; rhodopsin
    Language English
    Dates of publication 2020-0826
    Size p. 16023-16030.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.0c07264
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  8. Article ; Online: Potent bactericidal activity of reduced cryptdin-4 derived from its hydrophobicity and mediated by bacterial membrane disruption.

    Sato, Yuji / Wang, Yi / Song, Yuchi / Geng, Weiming / Yan, Shaonan / Nakamura, Kiminori / Kikukawa, Takashi / Demura, Makoto / Ayabe, Tokiyoshi / Aizawa, Tomoyasu

    Amino acids

    2022  Volume 54, Issue 2, Page(s) 289–297

    Abstract: Defensin is a cysteine-rich antimicrobial peptide with three disulphide bonds under normal oxidative conditions. Cryptdin-4 (Crp4) is a defensin secreted by Paneth cells in the small intestine of mice, and only reduced Crp4 ( ... ...

    Abstract Defensin is a cysteine-rich antimicrobial peptide with three disulphide bonds under normal oxidative conditions. Cryptdin-4 (Crp4) is a defensin secreted by Paneth cells in the small intestine of mice, and only reduced Crp4 (Crp4
    MeSH term(s) Amino Acid Sequence ; Animals ; Bacteria ; Hydrophobic and Hydrophilic Interactions ; Mice ; Protein Precursors ; alpha-Defensins/chemistry ; alpha-Defensins/pharmacology ; alpha-Defensins/physiology
    Chemical Substances Protein Precursors ; alpha-Defensins ; cryptdin (120668-29-3)
    Language English
    Publishing date 2022-01-17
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 1121341-3
    ISSN 1438-2199 ; 0939-4451
    ISSN (online) 1438-2199
    ISSN 0939-4451
    DOI 10.1007/s00726-021-03115-3
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  9. Article: Potent bactericidal activity of reduced cryptdin-4 derived from its hydrophobicity and mediated by bacterial membrane disruption

    Sato, Yuji / Wang, Yi / Song, Yuchi / Geng, Weiming / Yan, Shaonan / Nakamura, Kiminori / Kikukawa, Takashi / Demura, Makoto / Ayabe, Tokiyoshi / Aizawa, Tomoyasu

    Amino acids. 2022 Feb., v. 54, no. 2

    2022  

    Abstract: Defensin is a cysteine-rich antimicrobial peptide with three disulphide bonds under normal oxidative conditions. Cryptdin-4 (Crp4) is a defensin secreted by Paneth cells in the small intestine of mice, and only reduced Crp4 (Crp4ᵣₑd) shows activity ... ...

    Abstract Defensin is a cysteine-rich antimicrobial peptide with three disulphide bonds under normal oxidative conditions. Cryptdin-4 (Crp4) is a defensin secreted by Paneth cells in the small intestine of mice, and only reduced Crp4 (Crp4ᵣₑd) shows activity against enteric commensal bacteria, although both oxidised Crp4 (Crp4ₒₓ) and Crp4ᵣₑd can kill non-commensal bacteria. To investigate the molecular factors that affect the potent antimicrobial activity of Crp4ᵣₑd, the bactericidal activities of Crp4ₒₓ and Crp4ᵣₑd, Crp4 with all Cys residues substituted with Ser peptide (6C/S-Crp4), and Crp4 with all thiol groups modified by N-ethylmaleimide (NEM-Crp4) were assessed. All peptides showed bactericidal activity against non-commensal bacteria, whereas Crp4ᵣₑd and NEM-Crp4 showed bactericidal activity against commensal bacteria. These potent peptides exhibited high hydrophobicity, which was strongly correlated with membrane insertion. Intriguingly, Crp4ₒₓ formed electrostatic interactions with the membrane surface of bacteria, even without exerting bactericidal activity. Moreover, the bactericidal activity of both oxidised and reduced forms of Crp4 was abolished by inhibition of electrostatic interactions; this finding suggests that Crp4ᵣₑd targets bacterial membranes. Finally, a liposome leakage assay against lipids extracted from commensal bacteria demonstrated a correlation with bactericidal activity. These results suggest that the potent bactericidal activity of Crp4ᵣₑd is derived from its hydrophobicity, and the bactericidal mechanism involves disruption of the bacterial membrane. Findings from this study provide a better understanding of the bactericidal mechanism of both Crp4ₒₓ and Crp4ᵣₑd.
    Keywords antibacterial properties ; antimicrobial peptides ; disulfides ; hydrophobicity ; small intestine ; thiols
    Language English
    Dates of publication 2022-02
    Size p. 289-297.
    Publishing place Springer Vienna
    Document type Article
    ZDB-ID 1121341-3
    ISSN 1438-2199 ; 0939-4451
    ISSN (online) 1438-2199
    ISSN 0939-4451
    DOI 10.1007/s00726-021-03115-3
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  10. Article: A Basic Study of the Effects of Mulberry Leaf Administration to Healthy C57BL/6 Mice on Gut Microbiota and Metabolites.

    Gan, Li / Inamura, Yuga / Shimizu, Yu / Yokoi, Yuki / Ohnishi, Yuki / Song, Zihao / Kumaki, Yasuhiro / Kikukawa, Takashi / Demura, Makoto / Ito, Masaaki / Ayabe, Tokiyoshi / Nakamura, Kiminori / Aizawa, Tomoyasu

    Metabolites

    2023  Volume 13, Issue 9

    Abstract: Mulberry leaves contain α-glucosidase inhibitors, which have hypoglycemic effects and are considered functional foods. However, few reports have covered the effects of mulberry leaf components on normal gut microbiota and gut metabolites. Herein, gut ... ...

    Abstract Mulberry leaves contain α-glucosidase inhibitors, which have hypoglycemic effects and are considered functional foods. However, few reports have covered the effects of mulberry leaf components on normal gut microbiota and gut metabolites. Herein, gut microbiota analysis and NMR-based metabolomics were performed on the feces of mulberry leaf powder (MLP)-treated mice to determine the effects of long-term MLP consumption. Gut microbiota in the mouse were analyzed using 16S-rRNA gene sequencing, and no significant differences were revealed in the diversity and community structure of the gut microbiota in the C57BL/6 mice with or without MLP supplementation. Thirty-nine metabolites were identified via
    Language English
    Publishing date 2023-09-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo13091003
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