Next-generation single-molecule biophysics on ATP synthase

• Project/Area Number: 25251016
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics
• Research Institution: The University of Tokyo
• Principal Investigator: Noji Hiroyuki 東京大学, 工学(系)研究科(研究院), 教授 (00343111)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥47,060,000 (Direct Cost: ¥36,200,000、Indirect Cost: ¥10,860,000); Fiscal Year 2015: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000); Fiscal Year 2014: ¥14,950,000 (Direct Cost: ¥11,500,000、Indirect Cost: ¥3,450,000); Fiscal Year 2013: ¥21,840,000 (Direct Cost: ¥16,800,000、Indirect Cost: ¥5,040,000)
• Keywords: 1分子生物物理 / ナノバイオ / ATP合成酵素 / 生体エネルギー / マイクロチャンバー / 1分子計測 / 表面プラズモン / 膜チャンバー / トランスポーター / 1分子計測・操作 / 分子モーター / ＡＴＰ合成 / 表面増強ラマン / 1分子観察

Outline of Final Research Achievements

This project made two major achievements. The first is elucidation of molecular mechanism of F1-ATPase. The second is the development of novel single-molecule measurement techniques. The achievements in the first category include the elucidation of self-inactivation of F1-ATPase that is physiologically relevant. In collaboration with theorists, we revealed that angles for hydrolysis and inorganic phosphate release are different that have been thought to be the same. We also revealed the interaction of F1 with phosphate group of ATP directly leads torque generation. The novel single-molecule techniques developed in this project are nanorod imaging with ultra high spatiotemporal resolution and arrayed lipid bilayer chamber system (ALBiCs). Both of novel techniques were proved to be very powerful to bring new findings that have been not accessible with previous single molecule techniques.

Research Products

• [Journal Article] Novel nano-device to measure voltage-driven membrane transporter activity (2016)
  • Author(s): Watanabe, R., Soga, N., & Noji, H.
  • Journal Title: IEEE Transactions on Nanotechnology Volume: 15 Issue: 1 Pages: 70-73
  • DOI: 10.1109/tnano.2015.2498167
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] A single-molecule digital enzyme assay using alkaline phosphatase with a cumarin-based fluorogenic substrate (2015)
  • Author(s): Obayashi Y, Iino R, Noji H
  • Journal Title: Analyst Volume: 140 Issue: 15 Pages: 5065-6073
  • DOI: 10.1039/c5an00714c
  • Peer Reviewed / Open Access
• [Journal Article] Giant Acceleration of diffusion observed in a single-molecule experiment on F1-ATPase (2015)
  • Author(s): Hayashi R, Sasaki K, Nakamura S, Kudo S, Inoue Y, Noji H, Hayashi K
  • Journal Title: Physical Review letters Volume: 114
  • Peer Reviewed / Open Access
• [Journal Article] Attolitre-sized lipid bilayer chamber array for rapid detection of single transporters (2015)
  • Author(s): Soga, N., *Watanabe, R., & Noji, H.
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 11025-11025
  • DOI: 10.1038/srep11025
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Comprehensive chemical secretory measurement of single cells trapped in a micro-droplet array with mass spectrometry (2015)
  • Author(s): Hideaki Fujita, Tsuyoshi Esaki, Tsutomu Masujima, Akitsu Hotta, Soo Hyeon Kim, Hiroyuki Noji, Tomonobu M. Watanabe
  • Journal Title: RSC Adv. Volume: 5 Issue: 22 Pages: 16968-16971
  • DOI: 10.1039/c4ra12021c
  • Peer Reviewed / Open Access
• [Journal Article] Effects of an ATP analogue, adenosine 5′-[α-thio]-triphosphate, on F1-ATPase rotary catalysis, torque generation, and inhibited intermediated formation (2015)
  • Author(s): Yukawa A, Watanabe R and Noji H
  • Journal Title: Biochemical and Biophysical Research Communications Volume: 458 Issue: 3 Pages: 515-519
  • DOI: 10.1016/j.bbrc.2015.01.146
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] High-speed angle-resolved imaging of single gold nanorod with microsecond temporal resolution and one degree angle precision (2015)
  • Author(s): S. Enoki, R. Iino, Y. Niitani, Y. Minagawa, M. Tomishige, H. Noji
  • Journal Title: Anal. Chem. Volume: 87 Issue: 4 Pages: 2079-2086
  • DOI: 10.1021/ac502408c
  • Peer Reviewed / Open Access
• [Journal Article] Torque transmission mechanism via DELSEED loop of F1-ATPase (2015)
  • Author(s): Watanabe R, Koyasu K, You H, Tanigawara M and Noji H
  • Journal Title: Biophysical Journal Volume: 108 Issue: 5 Pages: 1144-1152
  • DOI: 10.1016/j.bpj.2015.01.017
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Single-molecule Imaging Analysis of Elementary Reaction Steps of Trichoderma reesei Cellobiohydrolase I (Cel7A) Hydrolyzing Crystalline Cellulose Iα and IIII (2014)
  • Author(s): Y.Shibafuji, A.Nakamura, T.Uchihashi, N.Sugimoto, S.Fukuda, H.Watanabe, M.Samejima, T.Ando, H.Noji, A.Koivula, K.Igarashi, R.Iino
  • Journal Title: Journal of Biological Chemistry Volume: 289 (29) Issue: 20 Pages: 1405614065-1405614065
  • DOI: 10.1074/jbc.m113.546085
  • Peer Reviewed / Open Access
• [Journal Article] Characterization of the temperature-sensitive reaction of F1-ATPase by using single molecule manipulation (2014)
  • Author(s): Watanabe R and Noji H
  • Journal Title: Scientific Reports Volume: 4 Issue: 1 Pages: 4962-4962
  • DOI: 10.1038/srep04962
  • Peer Reviewed / Open Access
• [Journal Article] Timing of inorganic phosphate release modulates the catalytic activity of ATP-driven rotary motor protein (2014)
  • Author(s): Watanabe R and Noji H
  • Journal Title: Nature Communications Volume: 5 Issue: 1 Pages: 3486-3486
  • DOI: 10.1038/ncomms4486
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] F1subunit reinforces torque generation in V-ATPase (2014)
  • Author(s): Junichi Kishikawa, Akihiko Seino, Atsuko Nakanishi, Naciye Esma Tirtom, Hiroyuki Noji, Ken Yokoyama, Kumiko Hayashi
  • Journal Title: European Biophysics Journal Volume: 43 Issue: 8-9 Pages: 415-422
  • DOI: 10.1007/s00249-014-0973-x
  • Peer Reviewed / Open Access
• [Journal Article] Torque generation mechanism of F1-ATPase upon NTP binding (2014)
  • Author(s): Arai HC, Yukawa A, Iwatate JR, Kamiya M, Watanabe R, Urano Y and Noji H
  • Journal Title: Biophys J Volume: 107 Issue: 1 Pages: 156-164
  • DOI: 10.1016/j.bpj.2014.05.016
  • Peer Reviewed / Open Access
• [Journal Article] Real-Time Fluorescence Visualization of Slow Tautomerization of Single Free-Base Phthalocyanines under Ambient Conditions (2014)
  • Author(s): Ikeda T, Iino R and Noji H
  • Journal Title: Chem. Commun Volume: 50 Issue: 67 Pages: 9443-9446
  • DOI: 10.1039/c4cc02574a
  • Peer Reviewed / Open Access
• [Journal Article] Motion Capture and Manipulation of Single Synthetic Molecular Rotors by Optical Microscopy (2014)
  • Author(s): Ikeda T, Tsukahara T, Iino R, Takeuchi M and Noji H
  • Journal Title: Angew.Chem.Int.Ed Volume: 53 Issue: 38 Pages: 10082-10085
  • DOI: 10.1002/ange.201403091
  • Peer Reviewed / Open Access
• [Journal Article] Robustness of the Rotary Catalysis Mechanism of F1-ATPase (2014)
  • Author(s): Watanabe R, Matsukage Y, Yukawa A, Tabata KV and Noji H
  • Journal Title: J Biol Chem Volume: 289 Issue: 28 Pages: 19331-19340
  • DOI: 10.1074/jbc.m114.569905
  • Peer Reviewed / Open Access
• [Journal Article] Arrayed lipid bilayer chambers allow single-molecule analysis of membrane transporter activity (2014)
  • Author(s): Watanabe R., Soga N., Fujita D., Tabata K. V., Yamauchi L., Kim S. H., Asanuma D., Kamiya M., Urano Y., Suga H. & Noji H.
  • Journal Title: Nature Communications Volume: 5 Issue: 1 Pages: 4519-4519
  • DOI: 10.1038/ncomms5519
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging (2014)
  • Author(s): Hideyuki Yaginuma, Shinnosuke Kawai, Kazuhito V. Tabata, Keisuke Tomiyama, Akira Kakizuka, Tamiki Komatsuzaki, Hiroyuki Noji, and Hiromi Imamura
  • Journal Title: Scientific Reports Volume: 4 Issue: 1 Pages: 6522-6522
  • DOI: 10.1038/srep06522
  • NAID: 120005575159
  • Peer Reviewed / Open Access
• [Journal Article] Thermodynamic analysis of F1-ATPase rotary catalysis using high-speed imaging (2014)
  • Author(s): Watanabe R, Minagawa Y and Noji H
  • Journal Title: Protein Science Volume: 23 Issue: 12 Pages: 1773-1779
  • DOI: 10.1002/pro.2559
  • Peer Reviewed / Open Access
• [Journal Article] Torque generation of Enterococcus hirae V-ATPase (2014)
  • Author(s): Ueno H, Minagawa Y, Hara M, Rahman S, Yamato I, Muneyuki E, Murata T, and Iino R
  • Journal Title: The Journal of Biological Chemistry Volume: 289 Issue: 45 Pages: 31212-31223
  • DOI: 10.1074/jbc.m114.598177
  • Peer Reviewed / Open Access
• [Journal Article] High-throughput formation of lipid bilayer membrane arrays with an asymmetric lipid composition (2014)
  • Author(s): Watanabe R., Soga N., Yamanaka T. & Noji H.
  • Journal Title: Scientific Reports Volume: 4 Issue: 1 Pages: 7076-7076
  • DOI: 10.1038/srep07076
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Key Chemical Factors of Arginine Finger Catalysis of F1-ATPase Clarified by an Unnatural Amino Acid Mutation (2014)
  • Author(s): Yukawa A, Iino R, Watanabe R, Hayashi S and Noji H
  • Journal Title: Biochemistry Volume: 54 Issue: 2 Pages: 472-480
  • DOI: 10.1021/bi501138b
  • Peer Reviewed / Open Access
• [Journal Article] Catalysis-enhancement via rotary fluctuation of F1-ATPase (2013)
  • Author(s): Watanabe R, Hayashi K, Ueno H and Noji H
  • Journal Title: Biophys. J Volume: 105 Issue: 10 Pages: 2385-2391
  • DOI: 10.1016/j.bpj.2013.09.050
  • Peer Reviewed
• [Journal Article] Glucose-stimulated single pancreatic islets sustain increased cytosolic ATP levels during initial Ca2+ influx and subsequent Ca2+ oscillations (2013)
  • Author(s): Tanaka T, Nagashima K, Inagaki N, Kioka H, Takashima S, Fukuoka H, Noji H, Kakizuka A and Imamura H
  • Journal Title: J Biol Chem Volume: 289 Issue: 4 Pages: 2205-2216
  • DOI: 10.1074/jbc.m113.499111
  • NAID: 120005689188
  • Peer Reviewed
• [Journal Article] Quantifying genetically inserted fluorescent protein in single iPS cells to monitor Nanog expression using electroactive microchamber arrays (2013)
  • Author(s): Kim SH, He X, Kaneda S, Kawada J, Fourmy D, Noji H and Fujii T
  • Journal Title: Lab on a Chip Volume: 14 Issue: 4 Pages: 730-736
  • DOI: 10.1039/c3lc51086g
  • Peer Reviewed
• [Journal Article] Evaluation of intra-mitochondrial ATP levels identifies G0/G1 switch gene 2 as a positive regulator of oxidative phosphorylation (2013)
  • Author(s): Kioka H, Kato H, Fujikawa M, Tsukamoto O, Suzuki T, Imamura H, Nakano A, Higo S, Yamazaki S, Matsuzaki T, Tkafuji K, Asanuma H, Asakura M, Minamino T, Shintani Y, Yoshida M, Noji H, Kitakaze M, Komuro I, Asano Y and Takashima S
  • Journal Title: PNAS Volume: 111 Issue: 1 Pages: 273-278
  • DOI: 10.1073/pnas.1318547111
  • Peer Reviewed / Open Access
• [Journal Article] Basic properties of rotary dynamics of the molecular motor Enterococcus hirae V1-ATPase (2013)
  • Author(s): Yoshihiro Minagawa, Hiroshi Ueno, Mayu Hara, Yoshiko Ishizuka-Katsura, Noboru Ohsawa,Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, Ichiro Yamato, Eiro Muneyuki, Hiroyuki Noji, Takeshi Murata, and Ryota Iino
  • Journal Title: J.Biol.Chem Volume: 288 Issue: 45 Pages: 32700-32707
  • DOI: 10.1074/jbc.m113.506329
  • Peer Reviewed
• [Journal Article] Single molecule analysis of the rotation of F1-ATPase under high hydrostatic pressure (2013)
  • Author(s): Daichi Okuno, Masayoshi Nishiyama and Hiroyuki Noji
  • Journal Title: Biophysical Journal Volume: 105 Issue: 7 Pages: 1635-1642
  • DOI: 10.1016/j.bpj.2013.08.036
  • NAID: 120005328380
  • Peer Reviewed
• [Journal Article] Single-molecule analysis of FoF1-ATP synthase inhibited by N,N-dicyclohexylcarbodiimide (2013)
  • Author(s): Toei M and Noji H
  • Journal Title: J Biol Chem Volume: 288 Issue: 36 Pages: 25717-25726
  • DOI: 10.1074/jbc.m113.482455
  • Peer Reviewed
• [Journal Article] In vivo fluorescent ATP imaging of Drosophila melanogaster and Caenorhabditis elegans by using a genetically encoded fluorescent ATP biosensor optimized for low temperatures. (2013)
  • Author(s): Tsuyama, Taiichi; Kishikawa, Jun-ichi; Han, Yong-Woon; Harada, Yoshie; Tsubouchi, Asako; Noji, Hiroyuki; Kakizuka, Akira; Yokoyama, Ken; Uemura, Tadashi; Imamura, Hiromi.
  • Journal Title: Analytical Chemistry Volume: 85(16) Issue: 16 Pages: 7889-7896
  • DOI: 10.1021/ac4015325
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Biased Brownian stepping rotation of FoF1-ATP synthase driven by proton motive force (2013)
  • Author(s): Watanabe R, Tabata KV, Iino R, Ueno H, Iwamoto M, Oiki S, Noji H
  • Journal Title: Nature Communications Volume: 4 Issue: 1 Pages: 1-6
  • DOI: 10.1038/ncomms2631
  • Peer Reviewed
• [Presentation] Single molecule analysis of transporter protein with arrayed lipid bilayer chamber (2015)
  • Author(s): Hiroyuki Noji
  • Organizer: Pacific Chem
  • Place of Presentation: Hawaii Convention Center（Honolulu, Hwaii, USA)
  • Year and Date: 2015-12-15
  • Int'l Joint Research / Invited
• [Presentation] Redesigning of F1-ATPase (2015)
  • Author(s): Hiroyuki Noji
  • Organizer: Pacific Chem
  • Place of Presentation: Hawaii Convention Center（Honolulu, Hwaii, USA)
  • Year and Date: 2015-12-15
  • Int'l Joint Research / Invited
• [Presentation] Single molecule biophysics of ATP synthase and digitalization revolution of bioassay (2015)
  • Author(s): Hiroyuki Noji
  • Organizer: POSTECH seminar
  • Place of Presentation: Pohang University of Science and Technology, Pohang-si, Korea
  • Year and Date: 2015-09-24
  • Int'l Joint Research / Invited
• [Presentation] Single-molecule biophysics on ATP synthase (2014)
  • Author(s): Hiroyuki Noji
  • Organizer: 2014 International Biophysics Congress(IUPAB2014)
  • Place of Presentation: Brisbane Convention & Exhibition Centre(Brisbane, Australia)
  • Year and Date: 2014-08-07
  • Invited
• [Presentation] Arrayed Lipid Bilayer Chamber for single-molecule analysis of transporters (2014)
  • Author(s): Hiroyuki Noji
  • Organizer: European Bioenergetics Conference(EBEC2014)
  • Place of Presentation: Faculdade de Ciencias(Lisbon, Portugal)
  • Year and Date: 2014-07-13
  • Invited
• [Presentation] Single-Molecule Digital ELISA and Prospects of its Applications (2014)
  • Author(s): Hiroyuki Noji
  • Organizer: World Lecture Series on Micro/Nanofluidics
  • Place of Presentation: Keio University(Kanagawa, Japana)
  • Year and Date: 2014-07-02
  • Invited
• [Presentation] Torque generation mechanism of F1-ATPase (2014)
  • Author(s): Hiroyuki Noji
  • Organizer: Tokyo ATPase Workshop(TAW)
  • Place of Presentation: The University of Tokyo (Tokyo, Japan)
  • Year and Date: 2014-06-02
  • Invited
• [Presentation] Recent advances of Single molecule biophysics of ATP synthase (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: The 8th International Conference on Advanced Mateials and Device
  • Place of Presentation: Korea, Jeju, Ramada Plaza Jeju Hotel
  • Invited
• [Presentation] Novel single-molecule systems to monitor the rotary dynamics and proton-pumping of FoF1-ATP synthase (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: ITALY IN JAPAN 2013 WORKSHOP (Methods for the investigation of ion transport machinery in biological Membranes)
  • Place of Presentation: 東京都、イタリア文化会館
  • Invited
• [Presentation] Single-molecule digital counting with femtoliter chamber array (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: International Symposium on Nanomedicine Molecular Science 2013
  • Place of Presentation: 東京都、東京大学
  • Invited
• [Presentation] Torque-generation mechanism of F1-ATPase (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: The 13th KIAS Conference on Protein Structure and Function
  • Place of Presentation: Korea、Seoul、Korea Institute for Advanced Study
  • Invited
• [Presentation] Single-Molecule counting of biomolecules with femtoliter dropret chamber array (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: The 17th International Conference on Solid-State Sensors
  • Place of Presentation: Spain, Barcelona, Barcelona International Convention Centre
  • Invited
• [Presentation] Single molecule biophysics of ATP synthase (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: Single Molecule Workshop
  • Place of Presentation: Taiwan, Taipei, , National Taicung University
  • Invited
• [Presentation] Single-Molecule Technology (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: Single-Molecule Biophysical Chemistry Workshop
  • Place of Presentation: Taiwan, Taipei, National Taiwan University
  • Invited
• [Presentation] Single-Molecule Biophysics of ATP synthase (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: Single-Molecule Biophysical Chemistry Workshop
  • Place of Presentation: Taiwan, Taipei, National Taiwan University
  • Invited
• [Presentation] Femtoliter chamber array for digital ELISA and single cell analysis (2013)
  • Author(s): Hiroyuki Noji
  • Organizer: Workshop on Technologies for Single Cell Analysis
  • Place of Presentation: 東京都、Hitachi Research Institute
  • Invited
• [Patent(Industrial Property Rights)] 高密度微小チャンバーアレイおよびその製造方法 (2013)
  • Inventor(s): 野地博行, 渡邉力也, 菅裕明, 藤田大士
  • Industrial Property Rights Holder: 野地博行, 渡邉力也, 菅裕明, 藤田大士
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2013-171493
  • Filing Date: 2013-08-21
• [Patent(Industrial Property Rights)] 検出装置及び検出方法 (2013)
  • Inventor(s): 野地博行、金秀炫、飯野亮太、太田淳、徳田崇、笹川清隆、野田俊彦
  • Industrial Property Rights Holder: 野地博行、金秀炫、飯野亮太、太田淳、徳田崇、笹川清隆、野田俊彦
  • Industrial Property Rights Type: 特許
  • Filing Date: 2013-08-29
  • Overseas