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  1. Article ; Online: Structural analysis of ATP bound to the F

    Todokoro, Yasuto / Miyasaka, Yoshiyuki / Yagi, Hiromasa / Kainosho, Masatsune / Fujiwara, Toshimichi / Akutsu, Hideo

    Biophysical chemistry

    2024  Volume 309, Page(s) 107232

    Abstract: ATP-hydrolysis-associated conformational change of the β-subunit during the rotation of ... ...

    Abstract ATP-hydrolysis-associated conformational change of the β-subunit during the rotation of F
    MeSH term(s) Proton-Translocating ATPases/chemistry ; Proton-Translocating ATPases/metabolism ; Hydrolysis ; Adenosine Triphosphate/metabolism ; Cryoelectron Microscopy ; Catalytic Domain ; Protein Conformation
    Chemical Substances Proton-Translocating ATPases (EC 3.6.3.14) ; Adenosine Triphosphate (8L70Q75FXE)
    Language English
    Publishing date 2024-04-03
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 185052-0
    ISSN 1873-4200 ; 0301-4622
    ISSN (online) 1873-4200
    ISSN 0301-4622
    DOI 10.1016/j.bpc.2024.107232
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  2. Article ; Online: Changes in the hydrophobic network of the FliG

    Nishikino, Tatsuro / Hijikata, Atsushi / Kojima, Seiji / Shirai, Tsuyoshi / Kainosho, Masatsune / Homma, Michio / Miyanoiri, Yohei

    iScience

    2023  Volume 26, Issue 8, Page(s) 107320

    Abstract: The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching rotational ... ...

    Abstract The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching rotational direction, the detailed molecular mechanism was not elucidated. Here, we studied the structural changes in the FliG fragment containing the middle and C-terminal regions, named FliG
    Language English
    Publishing date 2023-07-11
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.107320
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  3. Article ; Online: Conformational features and ionization states of Lys side chains in a protein studied using the stereo-array isotope labeling (SAIL) method.

    Takeda, Mitsuhiro / Miyanoiri, Yohei / Terauchi, Tsutomu / Kainosho, Masatsune

    Magnetic resonance (Gottingen, Germany)

    2021  Volume 2, Issue 1, Page(s) 223–237

    Abstract: Although both ... ...

    Abstract Although both the
    Language English
    Publishing date 2021-04-26
    Publishing country Germany
    Document type Journal Article
    ISSN 2699-0016
    ISSN (online) 2699-0016
    DOI 10.5194/mr-2-223-2021
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  4. Article: Recent developments in isotope-aided NMR methods for supramolecular protein complexes –SAIL aromatic TROSY

    Miyanoiri, Yohei / Kainosho, Masatsune / Takeda, Mitsuhiro / Terauchi, Tsutomu

    Biochimica et biophysica acta. 2020 Feb., v. 1864, no. 2

    2020  

    Abstract: The structure-function relationships for large protein complexes at the atomic level would be comprehensively understood, if hitherto unexplored aromatic ring NMR signals became accessible in addition to the currently used backbone amide and side-chain ... ...

    Abstract The structure-function relationships for large protein complexes at the atomic level would be comprehensively understood, if hitherto unexplored aromatic ring NMR signals became accessible in addition to the currently used backbone amide and side-chain methyl signals.The 82 kDa malate synthase G (MSG) proteins, selectively labeled with Trp and Phe bearing relaxation optimized isotope-labeled rings, were prepared to investigate the optimal conditions for obtaining the aromatic TROSY spectra.The MSG proteins, selectively labeled with either [δ1,ε1,ε3,η2]-SAIL Trp or ζ-SAIL Phe, provided well-separated, narrow TROSY signals for the 12 Trp and 19 Phe residues in MSG. The signals were assigned sequence-specifically, using the set of single amino acid substitution mutants. The site-specific substitution of each Phe with Tyr or Leu induced substantial chemical shifts for the other aromatic ring signals, allowing us to identify the aromatic clusters in MSG, which were comparable to the structural domains proposed previously.We demonstrated that the aromatic ring 13CH pairs without directly bonded 13C and adjacent 1H spins provide surprisingly narrow TROSY signals, if the rings are surrounded by fully deuterated amino acids. The observed signals can be readily assigned by either the single amino acid substitution or the NOEs between the aromatic and methyl protons, if the methyl assignments are available.The method described here should be generally applicable for difficult targets, such as proteins in lipid bilayers or possibly in living cells, thus providing unprecedented opportunities to use these new probes in structural biology.
    Keywords amino acid substitution ; amino acids ; aromatic compounds ; carbon ; isotope labeling ; lipid bilayers ; malate synthase ; mutants ; nuclear magnetic resonance spectroscopy ; proteins ; protons ; stable isotopes ; structural biology ; structure-activity relationships
    Language English
    Dates of publication 2020-02
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 840755-1
    ISSN 0304-4165
    ISSN 0304-4165
    DOI 10.1016/j.bbagen.2019.129439
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  5. Article: Chemical Conformation of the Essential Glutamate Site of the c-Ring within Thermophilic Bacillus FₒF₁-ATP Synthase Determined by Solid-State NMR Based on its Isolated c-Ring Structure

    Todokoro, Yasuto / Kang, Su-Jin / Suzuki, Toshiharu / Ikegami, Takahisa / Kainosho, Masatsune / Yoshida, Masasuke / Fujiwara, Toshimichi / Akutsu, Hideo

    Journal of the American Chemical Society. 2022 July 29, v. 144, no. 31

    2022  

    Abstract: Proton translocation through the membrane-embedded Fₒ component of F-type ATP synthase (FₒF₁) is facilitated by the rotation of the Fₒ c-subunit ring (c-ring), carrying protons at essential acidic amino acid residues. Cryo-electron microscopy (Cryo-EM) ... ...

    Abstract Proton translocation through the membrane-embedded Fₒ component of F-type ATP synthase (FₒF₁) is facilitated by the rotation of the Fₒ c-subunit ring (c-ring), carrying protons at essential acidic amino acid residues. Cryo-electron microscopy (Cryo-EM) structures of FₒF₁ suggest a unique proton translocation mechanism. To elucidate it based on the chemical conformation of the essential acidic residues of the c-ring in FₒF₁, we determined the structure of the isolated thermophilic Bacillus Fₒ (tFₒ) c-ring, consisting of 10 subunits, in membranes by solid-state NMR. This structure contains a distinct proton-locking conformation, wherein Asn23 (cN23) CᵞO and Glu56 (cE56) CᵟOH form a hydrogen bond in a closed form. We introduced stereo-array-isotope-labeled (SAIL) Glu and Asn into the tFₒc-ring to clarify the chemical conformation of these residues in tFₒF₁-ATP synthase (tFₒF₁). Two well-separated ¹³C signals could be detected for cN23 and cE56 in a 505 kDa membrane protein complex, respectively, thereby suggesting the presence of two distinct chemical conformations. Based on the signal intensity and structure of the tFₒc-ring and tFₒF₁, six pairs of cN23 and cE56 surrounded by membrane lipids take the closed form, whereas the other four in the a–c interface employ the deprotonated open form at a proportion of 87%. This indicates that the a–c interface is highly hydrophilic. The pKₐ values of the four cE56 residues in the a–c interface were estimated from the cN23 signal intensity in the open and closed forms and distribution of polar residues around each cE56. The results favor a rotation of the c-ring for ATP synthesis.
    Keywords H-transporting ATP synthase ; cryo-electron microscopy ; glutamic acid ; hydrogen bonding ; hydrophilicity ; membrane proteins
    Language English
    Dates of publication 2022-0729
    Size p. 14132-14139.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.2c03580
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  6. Article ; Online: Recent developments in isotope-aided NMR methods for supramolecular protein complexes -SAIL aromatic TROSY.

    Miyanoiri, Yohei / Takeda, Mitsuhiro / Terauchi, Tsutomu / Kainosho, Masatsune

    Biochimica et biophysica acta. General subjects

    2019  Volume 1864, Issue 2, Page(s) 129439

    Abstract: Background: The structure-function relationships for large protein complexes at the atomic level would be comprehensively understood, if hitherto unexplored aromatic ring NMR signals became accessible in addition to the currently used backbone amide and ...

    Abstract Background: The structure-function relationships for large protein complexes at the atomic level would be comprehensively understood, if hitherto unexplored aromatic ring NMR signals became accessible in addition to the currently used backbone amide and side-chain methyl signals.
    Methods: The 82 kDa malate synthase G (MSG) proteins, selectively labeled with Trp and Phe bearing relaxation optimized isotope-labeled rings, were prepared to investigate the optimal conditions for obtaining the aromatic TROSY spectra.
    Results: The MSG proteins, selectively labeled with either [δ
    Conclusions: We demonstrated that the aromatic ring
    General significance: The method described here should be generally applicable for difficult targets, such as proteins in lipid bilayers or possibly in living cells, thus providing unprecedented opportunities to use these new probes in structural biology.
    MeSH term(s) Carbon Isotopes ; Escherichia coli/enzymology ; Macromolecular Substances ; Magnetic Resonance Spectroscopy/methods ; Malate Synthase/chemistry ; Mutation ; Peptides/chemistry ; Phenylalanine/chemistry ; Protein Structure, Secondary ; Proteins/chemistry ; Protons ; Tryptophan/chemistry
    Chemical Substances Carbon Isotopes ; Macromolecular Substances ; Peptides ; Proteins ; Protons ; Phenylalanine (47E5O17Y3R) ; Tryptophan (8DUH1N11BX) ; Malate Synthase (EC 2.3.3.9) ; Carbon-13 (FDJ0A8596D)
    Language English
    Publishing date 2019-10-05
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 60-7
    ISSN 1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    ISSN (online) 1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    DOI 10.1016/j.bbagen.2019.129439
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  7. Article: [Recent advances in NMR methods for determining the structures and dynamics of larger proteins].

    Miyanoiri, Youhei / Takeda, Mitsuhiro / Kainosho, Masatsune

    Seikagaku. The Journal of Japanese Biochemical Society

    2018  Volume 88, Issue 4, Page(s) 452–464

    MeSH term(s) Animals ; Drug Design ; Nuclear Magnetic Resonance, Biomolecular/methods ; Protein Conformation ; Proteins/chemistry ; Structure-Activity Relationship
    Chemical Substances Proteins
    Language Japanese
    Publishing date 2018-04-04
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 282319-6
    ISSN 0037-1017
    ISSN 0037-1017
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  8. Article ; Online: Perspective: next generation isotope-aided methods for protein NMR spectroscopy.

    Kainosho, Masatsune / Miyanoiri, Yohei / Terauchi, Tsutomu / Takeda, Mitsuhiro

    Journal of biomolecular NMR

    2018  Volume 71, Issue 3, Page(s) 119–127

    Abstract: In this perspective, we describe our efforts to innovate the current isotope-aided NMR methodology to investigate biologically important large proteins and protein complexes, for which only limited structural information could be obtained by conventional ...

    Abstract In this perspective, we describe our efforts to innovate the current isotope-aided NMR methodology to investigate biologically important large proteins and protein complexes, for which only limited structural information could be obtained by conventional NMR approaches. At the present time, it is widely believed that only backbone amide and methyl signals are amenable for investigating such difficult targets. Therefore, our primary mission is to disseminate our novel knowledge within the biological NMR community; specifically, that any type of NMR signals other than methyl and amide groups can be obtained, even for quite large proteins, by optimizing the transverse relaxation properties by isotope labeling methods. The idea of "TROSY by isotope labeling" has been cultivated through our endeavors aiming to improve the original stereo-array isotope labeling (SAIL) method (Kainosho et al., Nature 440:52-57, 2006). The SAIL TROSY methods subsequently culminated in the successful observations of individual NMR signals for the side-chain aliphatic and aromatic
    MeSH term(s) Amino Acids ; Amino Acids, Aromatic ; Carbon Isotopes ; Isotope Labeling ; Nuclear Magnetic Resonance, Biomolecular/methods ; Protein Conformation
    Chemical Substances Amino Acids ; Amino Acids, Aromatic ; Carbon Isotopes
    Language English
    Publishing date 2018-06-22
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1081696-3
    ISSN 1573-5001 ; 0925-2738
    ISSN (online) 1573-5001
    ISSN 0925-2738
    DOI 10.1007/s10858-018-0198-x
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  9. Article ; Online: Chemical Conformation of the Essential Glutamate Site of the

    Todokoro, Yasuto / Kang, Su-Jin / Suzuki, Toshiharu / Ikegami, Takahisa / Kainosho, Masatsune / Yoshida, Masasuke / Fujiwara, Toshimichi / Akutsu, Hideo

    Journal of the American Chemical Society

    2022  Volume 144, Issue 31, Page(s) 14132–14139

    Abstract: Proton translocation through the membrane-embedded ... ...

    Abstract Proton translocation through the membrane-embedded F
    MeSH term(s) Adenosine Triphosphate/metabolism ; Bacillus/metabolism ; Cryoelectron Microscopy ; Glutamic Acid ; Protein Conformation ; Protein Subunits/chemistry ; Proton-Translocating ATPases/metabolism ; Protons
    Chemical Substances Protein Subunits ; Protons ; Glutamic Acid (3KX376GY7L) ; Adenosine Triphosphate (8L70Q75FXE) ; Proton-Translocating ATPases (EC 3.6.3.14)
    Language English
    Publishing date 2022-07-29
    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.2c03580
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  10. Article: [Achievement of Dr. Kurt Wuthrich, a winner of Nobel-Prize in 2002].

    Kainosho, Masatsune

    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme

    2003  Volume 48, Issue 1, Page(s) 59–62

    MeSH term(s) Biochemistry/history ; History, 20th Century ; History, 21st Century ; Macromolecular Substances ; Nobel Prize ; Nuclear Magnetic Resonance, Biomolecular/history ; Nucleic Acid Conformation ; Protein Conformation ; Proteomics/history
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2003-03-25
    Publishing country Japan
    Document type Biography ; Historical Article ; Journal Article ; Portrait
    ZDB-ID 391163-9
    ISSN 0039-9450
    ISSN 0039-9450
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