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  1. Article ; Online: Nuclear Magnetic Resonance Detection of Hydrogen Bond Network in a Proton Pump Rhodopsin RxR and Its Alteration during the Cyclic Photoreaction.

    Suzuki, Rika / Nagashima, Toshio / Kojima, Keiichi / Hironishi, Reika / Hirohata, Masafumi / Ueta, Tetsuya / Murata, Takeshi / Yamazaki, Toshio / Sudo, Yuki / Takahashi, Hideo

    Journal of the American Chemical Society

    2023  Volume 145, Issue 28, Page(s) 15295–15302

    Abstract: Hydrogen bond formation and deformation are crucial for the structural construction and functional expression of biomolecules. However, direct observation of exchangeable hydrogens, especially for oxygen-bound hydrogens, relevant to hydrogen bonds is ... ...

    Abstract Hydrogen bond formation and deformation are crucial for the structural construction and functional expression of biomolecules. However, direct observation of exchangeable hydrogens, especially for oxygen-bound hydrogens, relevant to hydrogen bonds is challenging for current structural analysis approaches. Using solution-state NMR spectroscopy, this study detected the functionally important exchangeable hydrogens (i.e., Y49-ηOH and Y178-ηOH) involved in the pentagonal hydrogen bond network in the active site of
    MeSH term(s) Rhodopsin/chemistry ; Proton Pumps/chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy
    Chemical Substances Rhodopsin (9009-81-8) ; Proton Pumps
    Language English
    Publishing date 2023-07-06
    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.3c02833
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations

    Yasuda, Satoshi / Akiyama, Tomoki / Kojima, Keiichi / Ueta, Tetsuya / Hayashi, Tomohiko / Ogasawara, Satoshi / Nagatoishi, Satoru / Tsumoto, Kouhei / Kunishima, Naoki / Sudo, Yuki / Kinoshita, Masahiro / Murata, Takeshi

    Journal of physical chemistry. 2022 Jan. 28, v. 126, no. 5

    2022  

    Abstract: We have developed a methodology for identifying further thermostabilizing mutations for an intrinsically thermostable membrane protein. The methodology comprises the following steps: (1) identifying thermostabilizing single mutations (TSSMs) for residues ...

    Abstract We have developed a methodology for identifying further thermostabilizing mutations for an intrinsically thermostable membrane protein. The methodology comprises the following steps: (1) identifying thermostabilizing single mutations (TSSMs) for residues in the transmembrane region using our physics-based method; (2) identifying TSSMs for residues in the extracellular and intracellular regions, which are in aqueous environment, using an empirical force field FoldX; and (3) combining the TSSMs identified in steps (1) and (2) to construct multiple mutations. The methodology is illustrated for thermophilic rhodopsin whose apparent midpoint temperature of thermal denaturation Tₘ is ∼91.8 °C. The TSSMs previously identified in step (1) were F90K, F90R, and Y91I with ΔTₘ ∼5.6, ∼5.5, and ∼2.9 °C, respectively, and those in step (2) were V79K, T114D, A115P, and A116E with ΔTₘ ∼2.7, ∼4.2, ∼2.6, and ∼2.3 °C, respectively (ΔTₘ denotes the increase in Tₘ). In this study, we construct triple and quadruple mutants, F90K+Y91I+T114D and F90K+Y91I+V79K+T114D. The values of ΔTₘ for these multiple mutants are ∼11.4 and ∼13.5 °C, respectively. Tₘ of the quadruple mutant (∼105.3 °C) establishes a new record in a class of outward proton pumping rhodopsins. It is higher than Tₘ of Rubrobacter xylanophilus rhodopsin (∼100.8 °C) that was the most thermostable in the class before this study.
    Keywords Rubrobacter xylanophilus ; amino acids ; denaturation ; membrane proteins ; mutants ; rhodopsin ; temperature ; thermal stability
    Language English
    Dates of publication 2022-0128
    Size p. 1004-1015.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021/acs.jpcb.1c08684
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Applicability of Styrene-Maleic Acid Copolymer for Two Microbial Rhodopsins, RxR and HsSRI.

    Ueta, Tetsuya / Kojima, Keiichi / Hino, Tomoya / Shibata, Mikihiro / Nagano, Shingo / Sudo, Yuki

    Biophysical journal

    2020  Volume 119, Issue 9, Page(s) 1760–1770

    Abstract: The membrane-embedded protein rhodopsin is widely produced in organisms as a photoreceptor showing a variety of light-dependent biological functions. To investigate its molecular features, rhodopsin is often extracted from cellular membrane lipids by a ... ...

    Abstract The membrane-embedded protein rhodopsin is widely produced in organisms as a photoreceptor showing a variety of light-dependent biological functions. To investigate its molecular features, rhodopsin is often extracted from cellular membrane lipids by a suitable detergent as "micelles." The extracted protein is purified by column chromatography and then is often reconstituted into "liposomes" by removal of the detergent. The styrene-maleic acid ("SMA") copolymer spontaneously forms nanostructures containing lipids without detergent. In this study, we applied SMA to characterize two microbial rhodopsins, a thermally stable rhodopsin, Rubrobacter xylanophilus rhodopsin (RxR), and an unstable one, Halobacterium salinarum sensory rhodopsin I (HsSRI), and evaluated their physicochemical properties in SMA lipid particles compared with rhodopsins in micelles and in liposomes. Those two rhodopsins were produced in Escherichia coli cells and were successfully extracted from the membrane by the addition of SMA (5 w/v %) without losing their visible color. Analysis by dynamic light scattering revealed that RxR in SMA lipid particles (RxR-SMA) formed a discoidal structure with a diameter of 54 nm, which was 10 times smaller than RxR in phosphatidylcholine liposomes. The small particle size of RxR-SMA allowed us to obtain scattering-less visible spectra with a high signal-to-noise ratio similar to RxR in detergent micelles composed of n-dodecyl-β-D-maltoside. High-speed atomic force microscopy revealed that a single particle contained an average of 4.1 trimers of RxR (12.3 monomers). In addition, RxR-SMA showed a fast cyclic photoreaction (k = 13 s
    MeSH term(s) Actinobacteria ; Halobacterium salinarum ; Maleates ; Rhodopsins, Microbial ; Styrene
    Chemical Substances Maleates ; Rhodopsins, Microbial ; Styrene (44LJ2U959V) ; maleic acid (91XW058U2C)
    Language English
    Publishing date 2020-09-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2020.09.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: Show issues Location:
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  4. Article ; Online: Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations.

    Yasuda, Satoshi / Akiyama, Tomoki / Kojima, Keiichi / Ueta, Tetsuya / Hayashi, Tomohiko / Ogasawara, Satoshi / Nagatoishi, Satoru / Tsumoto, Kouhei / Kunishima, Naoki / Sudo, Yuki / Kinoshita, Masahiro / Murata, Takeshi

    The journal of physical chemistry. B

    2022  Volume 126, Issue 5, Page(s) 1004–1015

    Abstract: We have developed a methodology for identifying further thermostabilizing mutations for an intrinsically thermostable membrane protein. The methodology comprises the following steps: (1) identifying thermostabilizing single mutations (TSSMs) for residues ...

    Abstract We have developed a methodology for identifying further thermostabilizing mutations for an intrinsically thermostable membrane protein. The methodology comprises the following steps: (1) identifying thermostabilizing single mutations (TSSMs) for residues in the transmembrane region using our physics-based method; (2) identifying TSSMs for residues in the extracellular and intracellular regions, which are in aqueous environment, using an empirical force field FoldX; and (3) combining the TSSMs identified in steps (1) and (2) to construct multiple mutations. The methodology is illustrated for thermophilic rhodopsin whose apparent midpoint temperature of thermal denaturation
    MeSH term(s) Amino Acids/genetics ; Mutation ; Proton Pumps/chemistry ; Protons ; Rhodopsin/genetics
    Chemical Substances Amino Acids ; Proton Pumps ; Protons ; Rhodopsin (9009-81-8)
    Language English
    Publishing date 2022-01-28
    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.1c08684
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Vectorial Proton Transport Mechanism of RxR, a Phylogenetically Distinct and Thermally Stable Microbial Rhodopsin.

    Kojima, Keiichi / Ueta, Tetsuya / Noji, Tomoyasu / Saito, Keisuke / Kanehara, Kanae / Yoshizawa, Susumu / Ishikita, Hiroshi / Sudo, Yuki

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 282

    Abstract: Rubrobacter xylanophilus rhodopsin (RxR) is a phylogenetically distinct and thermally stable seven-transmembrane protein that functions as a light-driven proton ( ... ...

    Abstract Rubrobacter xylanophilus rhodopsin (RxR) is a phylogenetically distinct and thermally stable seven-transmembrane protein that functions as a light-driven proton (H
    MeSH term(s) Actinobacteria/metabolism ; Hydrogen-Ion Concentration ; Mutagenesis, Site-Directed ; Protons ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/isolation & purification ; Rhodopsins, Microbial/chemistry ; Rhodopsins, Microbial/genetics ; Rhodopsins, Microbial/metabolism ; Sodium Chloride/chemistry
    Chemical Substances Protons ; Recombinant Proteins ; Rhodopsins, Microbial ; Sodium Chloride (451W47IQ8X)
    Language English
    Publishing date 2020-01-14
    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/s41598-019-57122-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained.

    Yasuda, Satoshi / Akiyama, Tomoki / Nemoto, Sayaka / Hayashi, Tomohiko / Ueta, Tetsuya / Kojima, Keiichi / Tsukamoto, Takashi / Nagatoishi, Satoru / Tsumoto, Kouhei / Sudo, Yuki / Kinoshita, Masahiro / Murata, Takeshi

    Journal of chemical information and modeling

    2020  Volume 60, Issue 3, Page(s) 1709–1716

    Abstract: We develop a new methodology best suited to the identification of thermostabilizing mutations for an intrinsically stable membrane protein. The recently discovered thermophilic rhodopsin, whose apparent midpoint temperature of thermal ... ...

    Abstract We develop a new methodology best suited to the identification of thermostabilizing mutations for an intrinsically stable membrane protein. The recently discovered thermophilic rhodopsin, whose apparent midpoint temperature of thermal denaturation
    MeSH term(s) Amino Acids ; Entropy ; Membrane Proteins/genetics ; Mutation ; Protein Conformation ; Temperature
    Chemical Substances Amino Acids ; Membrane Proteins
    Language English
    Publishing date 2020-03-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.0c00063
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
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