Hiroyuki Noji

Summary

Affiliation: Osaka University
Country: Japan

Publications

  1. ncbi request reprint [Nanoscience in rotary molecular motor proteins]
    Hiroyuki Noji
    Tanpakushitsu Kakusan Koso 52:297-300. 2007
  2. ncbi request reprint F1-ATPase changes its conformations upon phosphate release
    Tomoko Masaike
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226 8503, Japan
    J Biol Chem 277:21643-9. 2002
  3. ncbi request reprint Highly coupled ATP synthesis by F1-ATPase single molecules
    Yannick Rondelez
    LIMMS CNRS IIS, Tokyo 153 8505, Japan
    Nature 433:773-7. 2005
  4. pmc Temperature-sensitive reaction intermediate of F1-ATPase
    Rikiya Watanabe
    Department of Mechanical Engineering, University of Tokyo, Tokyo 113 8656, Japan
    EMBO Rep 9:84-90. 2008
  5. pmc Single-molecule study on the temperature-sensitive reaction of F1-ATPase with a hybrid F1 carrying a single beta(E190D)
    Sawako Enoki
    Institute of Scientific and Industrial Research, Osaka University, 567 0047 Osaka, Japan
    J Biol Chem 284:23169-76. 2009
  6. ncbi request reprint [Single molecule study on the mechano-chemical coupling of F1-ATPase motor by the use of an ultra small reaction chamber]
    Hiroyuki Noji
    Tanpakushitsu Kakusan Koso 52:302-8. 2007
  7. doi request reprint Mechanical modulation of catalytic power on F1-ATPase
    Rikiya Watanabe
    Department of Applied Chemistry, School of Engineering, University of Tokyo, Tokyo, Japan
    Nat Chem Biol 8:86-92. 2012
  8. doi request reprint Stiffness of γ subunit of F(1)-ATPase
    Daichi Okuno
    The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8 1, Ibaraki, Osaka, 567 0047, Japan
    Eur Biophys J 39:1589-96. 2010
  9. doi request reprint Phosphate release in F1-ATPase catalytic cycle follows ADP release
    Rikiya Watanabe
    Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
    Nat Chem Biol 6:814-20. 2010
  10. pmc Mechanical modulation of ATP-binding affinity of V1-ATPase
    Naciye Esma Tirtom
    Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113 8656, Japan
    J Biol Chem 288:619-23. 2013

Collaborators

Detail Information

Publications54

  1. ncbi request reprint [Nanoscience in rotary molecular motor proteins]
    Hiroyuki Noji
    Tanpakushitsu Kakusan Koso 52:297-300. 2007
  2. ncbi request reprint F1-ATPase changes its conformations upon phosphate release
    Tomoko Masaike
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226 8503, Japan
    J Biol Chem 277:21643-9. 2002
    ..This is the first evidence that the beta subunit changes its conformation upon phosphate release, which may share a common mechanism of exerting motility with other motor proteins...
  3. ncbi request reprint Highly coupled ATP synthesis by F1-ATPase single molecules
    Yannick Rondelez
    LIMMS CNRS IIS, Tokyo 153 8505, Japan
    Nature 433:773-7. 2005
    ..We provide here direct evidence that F1 is designed to tightly couple its catalytic reactions with the mechanical rotation. Our results suggest that the epsilon-subunit has an essential function during ATP synthesis...
  4. pmc Temperature-sensitive reaction intermediate of F1-ATPase
    Rikiya Watanabe
    Department of Mechanical Engineering, University of Tokyo, Tokyo 113 8656, Japan
    EMBO Rep 9:84-90. 2008
    ..Conversely, the addition of inorganic phosphate caused a pause at an angle of +80 degrees from that of the intermediate state. These observations strongly suggest that the newly found reaction intermediate is an ADP-releasing step...
  5. pmc Single-molecule study on the temperature-sensitive reaction of F1-ATPase with a hybrid F1 carrying a single beta(E190D)
    Sawako Enoki
    Institute of Scientific and Industrial Research, Osaka University, 567 0047 Osaka, Japan
    J Biol Chem 284:23169-76. 2009
    ..These findings suggest that the TS reaction is a structural rearrangement of beta before or after ATP binding...
  6. ncbi request reprint [Single molecule study on the mechano-chemical coupling of F1-ATPase motor by the use of an ultra small reaction chamber]
    Hiroyuki Noji
    Tanpakushitsu Kakusan Koso 52:302-8. 2007
  7. doi request reprint Mechanical modulation of catalytic power on F1-ATPase
    Rikiya Watanabe
    Department of Applied Chemistry, School of Engineering, University of Tokyo, Tokyo, Japan
    Nat Chem Biol 8:86-92. 2012
    ..Additionally, 9% of the ATP-driven rotary step was supported by thermal diffusion, suggesting that acceleration of the ATP docking process occurs via thermally agitated conformational fluctuations...
  8. doi request reprint Stiffness of γ subunit of F(1)-ATPase
    Daichi Okuno
    The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8 1, Ibaraki, Osaka, 567 0047, Japan
    Eur Biophys J 39:1589-96. 2010
    ..The estimated elasticity also partially explains the accommodation of the intrinsic step size mismatch between F(o) and F(1)-ATPase...
  9. doi request reprint Phosphate release in F1-ATPase catalytic cycle follows ADP release
    Rikiya Watanabe
    Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
    Nat Chem Biol 6:814-20. 2010
    ..These findings imply that under ATP synthesis conditions, P(i) binds to an empty catalytic site, preventing solution ATP (though not ADP) from binding. Thus, this supports the concept of selective ADP binding for efficient ATP synthesis...
  10. pmc Mechanical modulation of ATP-binding affinity of V1-ATPase
    Naciye Esma Tirtom
    Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113 8656, Japan
    J Biol Chem 288:619-23. 2013
    ..It was also suggested that shaft of V(1)-ATPase should be rotated at least 277° in a clockwise direction for efficient release of ATP under ATP-synthesis conditions...
  11. pmc Single-molecule analysis of inhibitory pausing states of V1-ATPase
    Naciye Esma Uner
    Department of Biotechnology, Osaka University, 1 3 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biol Chem 287:28327-35. 2012
    ..Mechanical activation largely depended on the direction and angular displacement of forced rotation, implying that V(1)-ATPase rotation modulates the off rate of ADP...
  12. ncbi request reprint A single-cell drug efflux assay in bacteria by using a directly accessible femtoliter droplet array
    Ryota Iino
    Department of Applied Chemistry, University of Tokyo, 7 3 1 Hongo, Tokyo 113 8656, Japan
    Lab Chip 12:3923-9. 2012
    ..Our approach will be a useful tool to screen novel pump inhibitors and efflux pump genes, and to overcome infectious diseases caused by multi-drug-resistant bacteria...
  13. pmc Role of the DELSEED loop in torque transmission of F1-ATPase
    Mizue Tanigawara
    Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan
    Biophys J 103:970-8. 2012
    ..Our results emphasize the importance of loop rigidity for efficient torque transmissions...
  14. ncbi request reprint Operation mechanism of F(o) F(1)-adenosine triphosphate synthase revealed by its structure and dynamics
    Ryota Iino
    Department of Applied Chemistry, University of Tokyo, Bunkyo ku, Tokyo, Japan
    IUBMB Life 65:238-46. 2013
    ..In this critical review, we summarize our latest knowledge about the operation mechanism of this sophisticated nanomachine, revealed by its structure and dynamics...
  15. doi request reprint Highly sensitive restriction enzyme assay and analysis: a review
    Liza Lam
    The Institute of Scientific and Industrial Research, Osaka University, Osaka 567 0047, Japan
    Anal Bioanal Chem 391:2423-32. 2008
    ..Finally, we take a brief look at the general trends in technological development in this field by comparing the advantages and disadvantages of performing assays at bulk, microscale and single-molecule levels...
  16. pmc Simple dark-field microscopy with nanometer spatial precision and microsecond temporal resolution
    Hiroshi Ueno
    Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
    Biophys J 98:2014-23. 2010
    ..1-mus temporal resolution. Because of the simple optics, this system will be applicable to various biophysical studies requiring high spatial and temporal resolution in vitro and also in vivo...
  17. ncbi request reprint Chemomechanical coupling in single-molecule F-type ATP synthase
    Ryota Iino
    The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
    J Bioenerg Biomembr 37:451-4. 2005
    ..It is plausible that the conformational change of epsilon switches the catalytic mode of F(0)F(1) for highly coupled ATP synthesis...
  18. pmc Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation
    Daichi Okuno
    The Institute of Scientific and Industrial Research, Osaka University, 8 1 Mihogaoka, Ibaraki, Osaka 567 0047, Japan
    Proc Natl Acad Sci U S A 105:20722-7. 2008
    ..The former point was again confirmed in experiments where F(1) rotation was inhibited by adenosine-5'-(beta,gamma-imino)-triphosphate and/or azide, the most commonly used inhibitors for the crystallization of F(1)...
  19. ncbi request reprint Fluctuation theorem applied to F1-ATPase
    Kumiko Hayashi
    The Institute of Scientific and Industrial Research, Osaka University, 8 1 Mihogaoka, Ibaraki 567 0047, Osaka, Japan
    Phys Rev Lett 104:218103. 2010
    ..We found that FT provided the better estimation of the rotary torque of F1 than the conventional method...
  20. doi request reprint Large-scale femtoliter droplet array for digital counting of single biomolecules
    Soo Hyeon Kim
    Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Hongo 7 3 1, Bunkyo ku, Tokyo 113 8656, Japan
    Lab Chip 12:4986-91. 2012
    ..Our digital counting device using one million droplets has great potential as a highly sensitive, portable immunoassay device that could be used to diagnose diseases...
  21. doi request reprint Chemomechanical coupling mechanism of F(1)-ATPase: catalysis and torque generation
    Rikiya Watanabe
    Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113 8656, Japan
    FEBS Lett 587:1030-5. 2013
    ..The energy conversion mechanism of F1 elucidated from single-molecule studies provides us with important insights into the operating principles underlying molecular motors...
  22. pmc Mechanism of inhibition by C-terminal alpha-helices of the epsilon subunit of Escherichia coli FoF1-ATP synthase
    Ryota Iino
    Institute of Scientific and Industrial Research, Osaka University, 567 0047 Osaka, Japan
    J Biol Chem 284:17457-64. 2009
    ..These results suggest that the C-terminal domain of the epsilon subunit of EFoF1 slows multiple elementary steps in both the ATP synthesis/hydrolysis reactions by restricting the rotation of the gamma subunit...
  23. doi request reprint Acceleration of the ATP-binding rate of F1-ATPase by forcible forward rotation
    Yuko Iko
    Institute of Scientific and Industrial Science, Osaka University, Mihogaoka 8 1, Ibaraki, Osaka 567 0047, Japan
    FEBS Lett 583:3187-91. 2009
    ..Here, we report direct evidence that the ATP-binding rate of F1 increases upon the forward rotation of the rotor, and its binding affinity to ATP is enhanced by rotation...
  24. pmc Principal role of the arginine finger in rotary catalysis of F1-ATPase
    Yoshihito Komoriya
    Graduate School of Frontier Bioscience, Osaka University, 1 3 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biol Chem 287:15134-42. 2012
    ..Lysine substitution also caused frequent pauses because of severe ADP inhibition, and a slight decrease in ATP-binding rate...
  25. doi request reprint A single-molecule enzymatic assay in a directly accessible femtoliter droplet array
    Shouichi Sakakihara
    Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, 8 1, Ibaraki, Osaka 567 0047, Japan
    Lab Chip 10:3355-62. 2010
    ..Using these advantages, we successfully measured the kinetic parameters of the single-molecule enzyme β-galactosidase and rotary motor protein F(1)-ATPase enclosed in a droplet...
  26. doi request reprint Loop-mediated isothermal amplification of a single DNA molecule in polyacrylamide gel-based microchamber
    Liza Lam
    The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
    Biomed Microdevices 10:539-46. 2008
    ....
  27. pmc Winding single-molecule double-stranded DNA on a nanometer-sized reel
    Huijuan You
    Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo ku, Tokyo 113 8656, Japan
    Nucleic Acids Res 40:e151. 2012
    ....
  28. pmc Activation of pausing F1 motor by external force
    Yoko Hirono-Hara
    Institute of Industrial Science and Precursory Research for Embryonic Science and Technology, Japan Science and Technology Corporation, University of Tokyo, Tokyo 153 8505, Japan
    Proc Natl Acad Sci U S A 102:4288-93. 2005
    ..Furthermore, the mechanical work for the forced rotation was efficiently converted into work for expelling ADP from the catalytic site, supporting the tight coupling between the rotation and catalytic event...
  29. doi request reprint Intersubunit coordination and cooperativity in ring-shaped NTPases
    Ryota Iino
    Department of Applied Chemistry, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 8656, Japan
    Curr Opin Struct Biol 23:229-34. 2013
    ..Here, we discuss these models and introduce high-speed atomic force microscopy as a new potent tool for verification of the model, with our recent example of the rotary catalysis of the stator ring of F1-adenosine triphosphatase...
  30. pmc Single-molecule analysis of F0F1-ATP synthase inhibited by N,N-dicyclohexylcarbodiimide
    Masashi Toei
    Department of Applied Chemistry, School of Engineering, University of Tokyo, Tokyo 113 8656, Japan
    J Biol Chem 288:25717-26. 2013
    ..This effect could be caused by balancing the angular positions of the F1 and the F0 rotors, which are connected via elastic elements. ..
  31. doi request reprint Measurement of the conformational state of F(1)-ATPase by single-molecule rotation
    Daichi Okuno
    The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
    Methods Enzymol 475:279-96. 2010
    ..A protocol for inhibition of the wild-type F(1) with chemical inhibitors such as adenosine-5'-(beta,gamma-imino)-triphosphate (AMP-PNP) or/and N(3)(-) under crystallization conditions is also provided...
  32. doi request reprint Ca²⁺ regulation of mitochondrial ATP synthesis visualized at the single cell level
    Masahiro Nakano
    Institute of Scientific and Industrial Research, Osaka University, Japan
    ACS Chem Biol 6:709-15. 2011
    ..Also, the GO-ATeam excitation wavelength is much less phototoxic to cells, making the probe suitable for long-time observation...
  33. pmc Evaluation of multidrug efflux pump inhibitors by a new method using microfluidic channels
    Yoshimi Matsumoto
    Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
    PLoS ONE 6:e18547. 2011
    ..The new method clarified that D13-9001 specifically inhibited MexAB-OprM in contrast to PAβN, which appeared to be a substrate of the pumps and permeabilized the membranes in E. coli...
  34. pmc Visualization of cargo concentration by COPII minimal machinery in a planar lipid membrane
    Kazuhito V Tabata
    Department of Biomolecular Energetics, The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
    EMBO J 28:3279-89. 2009
    ..We propose that the minimal set of COPII components is required not only to concentrate cargo molecules, but also to mediate exclusion of non-cargo proteins from the COPII vesicles...
  35. pmc Timing of inorganic phosphate release modulates the catalytic activity of ATP-driven rotary motor protein
    Rikiya Watanabe
    1 Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo ku, Tokyo 113 8656, Japan 2 PRESTO, JST, Bunkyo ku, Tokyo 113 8656, Japan
    Nat Commun 5:3486. 2014
    ..This inactive state presents MgADP inhibition, and thus, we find that an improper reaction sequence of F1-ATPase catalysis induces MgADP inhibition. ..
  36. ncbi request reprint An integrated system for enzymatic cleavage and electrostretching of freely-suspended single DNA molecules
    Liza Lam
    The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, 8 1, Ibaraki, 567 0047, Japan
    Lab Chip 7:1738-45. 2007
    ..Furthermore, with the employment of porous polyacrylamide gel, the effective manipulation of DNA assays and the ability to combine conventionally independent bioanalytical processes have been demonstrated...
  37. pmc Characterization of the temperature-sensitive reaction of F1-ATPase by using single-molecule manipulation
    Rikiya Watanabe
    1 Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo ku, Tokyo 113 8656, Japan 2 PRESTO, JST, Bunkyo ku, Tokyo 113 8656, Japan
    Sci Rep 4:4962. 2014
    ..Thus, we confirmed that the TS reaction contributes significantly to the rotation of F1. ..
  38. ncbi request reprint Simultaneous optical and electrical single channel recordings on a PEG glass
    Toru Ide
    Soft Biosystem Group, Laboratories for Nanobiology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
    Langmuir 26:8540-3. 2010
    ..The channels were immobilized in the membranes by anchoring to PEG molecules on the glass. The technique developed in this study should pave the way for single molecule pharmacology of ion-channels...
  39. ncbi request reprint [Molecular mechanism of torque generation in F1-motor]
    Hiroyuki Noji
    Tanpakushitsu Kakusan Koso 47:1174-81. 2002
  40. ncbi request reprint Stepping rotation of F(1)-ATPase with one, two, or three altered catalytic sites that bind ATP only slowly
    Takayuki Ariga
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226 8503, Japan
    J Biol Chem 277:24870-4. 2002
    ....
  41. pmc Single molecule energetics of F1-ATPase motor
    Eiro Muneyuki
    Department of Physics, Faculty of Science and Technology, Chuo University, Tokyo, Japan
    Biophys J 92:1806-12. 2007
    ..The results imply that microscopically defined work at a single molecule level cannot be directly compared with macroscopically defined free energy input...
  42. ncbi request reprint [Methods for visualization of a single molecule of rotating molecular motor in living organisms]
    Yoko Hara
    Nihon Seirigaku Zasshi 65:179-84. 2003
  43. ncbi request reprint Origin of apparent negative cooperativity of F(1)-ATPase
    Sakurako Ono
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, 226 8503 Yokohama, Japan
    Biochim Biophys Acta 1607:35-44. 2003
    ..Thus, the frequently observed K(m)'s of 100-300 microM and 1-30 microM range for wild-type F(1)-ATPase correspond to ATP binding to a noncatalytic site and catalytic site, respectively...
  44. ncbi request reprint Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation
    Kengo Adachi
    Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku ku, Tokyo 169 8555, Japan
    Cell 130:309-21. 2007
    ..This and other results suggest that the affinity for ADP also decreases with rotation, and thus ADP release contributes part of energy for rotation. Together with previous results, the coupling scheme is now basically complete...
  45. ncbi request reprint Chemomechanical coupling in F1-ATPase revealed by simultaneous observation of nucleotide kinetics and rotation
    Takayuki Nishizaka
    Kansai Advanced Research Center, Protein Biophysics Group, Iwaoka 588 2, Nishi ku, Kobe 651 2492, Japan
    Nat Struct Mol Biol 11:142-8. 2004
    ....
  46. ncbi request reprint Mechanically driven ATP synthesis by F1-ATPase
    Hiroyasu Itoh
    Tsukuba Research Laboratory, Hamamatsu Photonics KK, Joko, Hamamatsu 431 3103, Japan
    Nature 427:465-8. 2004
    ..This shows that a vectorial force (torque) working at one particular point on a protein machine can influence a chemical reaction occurring in physically remote catalytic sites, driving the reaction far from equilibrium...
  47. ncbi request reprint Visualization of RecA filaments and DNA by fluorescence microscopy
    Taro Nishinaka
    Yashima Super structured Helix Project, ERATO, Japan Science and Technology Agency, 101 Creation Core Nagoya, 2266 22 Anagahora, Nagoya 463 0003, Japan
    J Biochem 141:147-56. 2007
    ..We showed that the RecA-DNA filament disassembled in the direction from 5' to 3' of ssDNA as dATP hydrolysis proceeded...
  48. doi request reprint Photo gel-sol/sol-gel transition and its patterning of a supramolecular hydrogel as stimuli-responsive biomaterials
    Shinji Matsumoto
    Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo ku, Kyoto, 615 8510, Japan
    Chemistry 14:3977-86. 2008
    ..These results demonstrated that the photoresponsive supramolecular hydrogel and the resulting nanomeshes may provide unique biomaterials for the spatiotemporal manipulation of various biomolecules and live bacteria...
  49. pmc Evidence for rotation of V1-ATPase
    Hiromi Imamura
    ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation, 5800 3 Nagatsuta, Midori ku, Yokohama 226 0026, Japan
    Proc Natl Acad Sci U S A 100:2312-5. 2003
    ..This study provides experimental evidence that V(o)V(1)-ATPase is a rotary motor and that both D and F subunits constitute a rotor shaft...
  50. ncbi request reprint Single-molecule imaging of rotation of F1-ATPase
    Kengo Adachi
    Center for Integrative Bioscience, Okazaki National Research Institutes, Okazaki, Aichi 444 8585, Japan
    Methods Enzymol 361:211-27. 2003
  51. pmc The ATP-waiting conformation of rotating F1-ATPase revealed by single-pair fluorescence resonance energy transfer
    Ryohei Yasuda
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 100:9314-8. 2003
    ....
  52. ncbi request reprint Microfabricated arrays of femtoliter chambers allow single molecule enzymology
    Yannick Rondelez
    Nat Biotechnol 23:361-5. 2005
    ..The approach should be of interest for many ultrasensitive bioassays at the single-molecule level...
  53. ncbi request reprint Micro patterning of active proteins with perforated PDMS sheets (PDMS sieve)
    Kyoko Atsuta
    Center for International Research on Micro Mechatronics CIRMM, Institute of Industrial Science, University of Tokyo, 4 6 1 Komaba, Meguro ku, Tokyo 153 8505, Japan
    Lab Chip 4:333-6. 2004
    ..Selective patterning with three kinds of fluorescent micro beads indicated the possibility of patterning of different proteins on the same substrate by using the sieve...
  54. ncbi request reprint Thermally responsive supramolecular nanomeshes for on/off switching of the rotary motion of F1-ATPase at the single-molecule level
    Satoshi Yamaguchi
    PRESTO Synthesis and Control, JST, Kyoto University, Katsura, Nishikyo ku, Kyoto, 615 8510, Japan
    Chemistry 14:1891-6. 2008
    ..The integration of biomolecules and hard materials, interfaced with intelligent soft materials such as supramolecular hydrogels, is promising for the development of novel semi-synthetic nano-biodevices...