Original Papers Review Articles Talks/Patents


71. *Harashima T, Otomo A, *Iino R
Mechanism-based design of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins
bioRxiv DOI:10.1101/2024.05.23.595615


70. Matsumoto Y, Yamasaki S, Hayama K, Iino R, Noji H, Yamaguchi A, *Nishino K
Changes in the expression of mexB, mexY, and oprD in clinical Pseudomonas aeruginosa isolates
Proc Jpn Acad Ser B 100, 57-67 (2024) DOI:10.2183/pjab.100.006

69. *Nishida J, Otomo A, Koitaya T, Shiotari A, Minato T, Iino R, and *Kumagai T
Sub-tip-radius near-field interactions in nano-FTIR vibrational spectroscopy on single proteins
Nano Lett 24, 836–843 (2024) DOI:10.1021/acs.nanolett.3c03479
Press release: Observing single protein with infrared nanospectroscopy
プレスリリース: 赤外光で単一のタンパク質を見る新技術


68. Burton-Smith RN, Song C, Ueno H, Murata T, Iino R, *Murata K
Six states of Enterococcus hirae V-type ATPase reveals non-uniform rotor rotation during turnover
Commun Biol 6, Article number 755 (2023) DOI:10.1038/s42003-023-05110-8
bioRxiv (2022) DOI: 10.1101/2022.08.09.503272
Pressre relase: The structures of six states of a rotary sodium ion pump are revealed

67. *Kosugi T, Iida T, Tanabe M, Iino R, *Koga N
Design of allosteric sites into rotary motor V1-ATPase by restoring lost function of pseudo-active sites
Nature Chemistry 15, 1591–1598 (2023) DOI:10.1038/s41557-023-01256-4
Preprint: bioRxiv (2020) DOI: 10.1101/2020.09.09.288571
Pressre relase: Scientists develop strategy to engineer artificial allosteric sites in protein complexes
プレスリリース:進化の過程で失った機能を復活させ、回転型分子モーターの加速に成功 ~タンパク質複合体の協奏的機能を制御する新手法~


66. Otomo A, Iida T, Okuni Y, Ueno H, Murata T, *Iino R
Direct Observation of Stepping Rotation of V-ATPase Reveals Rigid Component in Coupling between Vo and V1 Motors
Proc Natl Acad Sci USA 119, e2210204119 (2022) DOI: 10.1073/pnas.2210204119
Preprint: bioRxiv (2022) DOI: 10.1101/2022.06.13.494302
Press release "Molecular-motor specialists deepen our understanding of a rotary ion pump of the cell"



65. *Nakamura A, Kobayashi N, Koga N, *Iino R
Positive charge introduction on the surface of thermostabilized PET hydrolase facilitates PET binding and degradation
ACS Catalysis 11, 8550-8564 (2021) DOI: 10.1021/acscatal.1c01204
Press release "Engineered protein inspired by nature may help plastic plague"
プレスリリース1: プラスチック分解酵素の熱安定性と活性を向上させ、熱安定性向上の構造的基盤と活性向上の機構を解明(2021年7月1日)
科学新聞:プラスチック分解酵素 熱安定性と活性を向上(2021年7月23日)
プレスリリース2: “酵素でペットボトルをリサイクル” PET分解酵素の産業応用に向けた共同研究を開始(2022年1月18日)
Press release 2: Joint Research Begins on PET-degrading Enzymes for Sustainable Recycling (2022/1/31)
日刊工業新聞(PDF):酵素でペットボトル再生 キリン静岡大など共同研究(2022年1月20日24面、転載許諾済)


64. Ando J, Kawagoe H, Nakamura A, Iino R, *Fujita K
Label-free monitoring of crystalline chitin hydrolysis by chitinase based on Raman spectroscopy
Analyst 146, 4087-4094 (2021) DOI: 10.1039/D1AN00581B



63. Visootsat A, Nakamura A, Wang T-W, *Iino R
Combined approach to engineer a highly active mutant of processive chitinase hydrolyzing crystalline chitin
ACS Omega 5, 26807–26816 (2020) DOI: 10.1021/acsomega.0c03911 OA


62. *Nakamura A, Ishiwata D, Visootsat A, Uchiyama T, Mizutani K, Kaneko S, Murata T, Igarashi K, *Iino R
Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases
J Biol Chem 295, 14606-14617 (2020) DOI: 10.1074/jbc.RA120.014792 OA
Press release in EurekAlert


61. *Yamaguchi S, Takagi R, Hosogane T, Ohashi Y, Sakai Y, Sakakihara S, Iino R, Tabata KV, Noji H, *Okamoto A
Single cell array enclosed with a photodegradable hydrogel in microwells for image-based cell classification and selective photorelease of cells
ACS Appl. Bio Mater 3, 5887–5895 (2020) DOI: 10.1021/acsabm.0c00583


60. *Okazaki K, Nakamura A, Iino R
Chemical-state-dependent free energy profile from single-molecule trajectories of biomolecular motor: Application to processive chitinase
J Phys Chem B 124, 6475–6487 (2020) DOI: 10.1021/acs.jpcb.0c02698
Press release in EurekAlert
プレスリリース:分子モーターの1方向性運動モデルの新規推定法の開発 ―キチナーゼの運動メカニズム解明につながる―
科学新聞:分子モーターの1方向性運動:推定法の開発 分子研など成果(2020年8月28日6面)


59. Ando J, Shima T, Kanazawa R, Shimo-Kon R, Nakamura A, Yamamoto M, Kon T, *Iino R
Small stepping motion of processive dynein revealed by load-free high-speed single-particle tracking
Sci Rep 10, Article number: 1080 (2020) DOI: 10.1038/s41598-020-58070-y OA
Press release in EurekAlert
オプトロニクスオンライン:分子研ら,レーザー顕微鏡で分子モーターを1分子観察 (2020年1月27日)
科学新聞:リニア分子モーター「ダイニン」 二足で歩行「まるで酔っ払い」(2020年2月14日6面)


58. Visootsat A, Nakamura A, Vignon P, Watanabe H, Uchihashi T, *Iino R
Single-molecule imaging analysis reveals the mechanism of a high-catalytic-activity mutant of chitinase A from Serratia marcescens
J Biol Chem 295, 1915-1925 (2020) DOI: 10.1074/jbc.RA119.012078 OA


57. #Umakoshi T, #Fukuda S, Iino R, Uchihashi T, *Ando T (#Equal contribution)
High-speed near-field fluorescence microscopy combined with high-speed atomic force microscopy for biological studies
BBA General Subjects 1864, 129325 (2020) DOI: 10.1016/j.bbagen.2019.03.011



56. *Ando J, Nakamura A, Yamamoto M, Song C, Murata K, *Iino R
Multicolor high-speed tracking of single biomolecules with silver, gold, silver-gold alloy nanoparticles
ACS Photonics 6, 2870-2883 (2019) DOI: 10.1021/acsphotonics.9b00953
Press release in EurekAlert
Optics & Photonics News: Nanoparticles Enable Multicolor Imaging of Biomolecules
Antpedia: 原来纳米粒子可以对生物分子进行多色成像
オプトロニクスオンライン:分子研ら,光学顕微鏡でマルチカラー1分子観察 (2019年11月26日)
科学新聞:マルチカラー高速高精度1分子観察 分子研が光学顕微鏡で実現


55. Iida T, Minagawa Y, Ueno H, Kawai F, Murata T, *Iino R
Single-molecule analysis reveals rotational substeps and chemo-mechanical coupling scheme of Enterococcus hirae V1-ATPase
J Biol Chem 294, 17017-17030 (2019) DOI: 10.1074/jbc.RA119.008947 OA
Press release in EurekAlert


54. *Zhang Y, Minagawa Y, Kizoe H, Miyazaki K, Iino R, Ueno H, Tabata KV, Shimane Y, *Noji H
Accurate high-throughput screening based on digital protein synthesis in a massively parallel femtoliter droplet array
Sci Adv 5, eaav8185 (2019) DOI: 10.1126/sciadv.aav8185 OA
Research introduction by Yi Zhang (JAMSTEC)



53. #Ando J, #Nakamura A, Visootsat A, Yamamoto M, Song C, Murata K, *Iino R (#Equal contribution)
Single-nanoparticle tracking with angstrom localization precision and microsecond time resolution
Biophys J 115: 2413-2427 (2018) DOI: 10.1016/j.bpj.2018.11.016 OA
Press release in EurekAlert
科学新聞紹介記事(2018年12月14日1面、pdf 0.8MB)


52. Fujimoto K, Morita Y, Iino R, Tomishige M, Shintaku H, Kotera H, *Yokokawa R
Simultaneous observation of kinesin-driven microtubule motility and binding of adenosine triphosphate using linear zero-mode waveguides
ACS Nano 12: 11975–11985 (2018) DOI: 10.1021/acsnano.8b03803
プレスリリース:モータータンパク質とATPの結合を1分子で可視化することに成功 ナノ構造に閉じ込めた光でモータータンパク質の仕組みに迫る
科学新聞紹介記事(2018年12月21日4面、pdf 1MB)


51. Tsunoda J, Song C, Lica Imai F, Takagi J, Ueno H, Murata T, Iino R, *Murata K
Off-axis rotor in Enterococcus hirae V-ATPase visualized by Zernike phase plate single-particle cryo-electron microscopy
Sci Rep 8: 15632 (2018) DOI: 10.1038/s41598-018-33977-9 OA


50. *Nakamura A, Okazaki K, Furuta T, Sakurai M, *Iino R
Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin
Nat Commun. 9: 3814 (2018) DOI: 10.1038/s41467-018-06362-3 OA
Press release in EurekAlert
科学新聞紹介記事(2018年10月5日6面、pdf 1MB)


49. Kawai F, Nakamura A, Visootsat A, *Iino R
Plasmid-based one-pot saturation mutagenesis and robot-based automated screening for protein engineering
ACS Omega 3: 7715–7726 (2018) DOI: 10.1021/acsomega.8b00663 OA


48. #Uchihashi T, #*Watanabe YH, Nakazaki Y, Yamasaki T, Watanabe T, Maruno T, Ishii K, Uchiyama S, Song C, Murata K, *Iino R, *Ando T (#Equal contribution)
Dynamic structural states of ClpB involved in its disaggregation function
Nat Commun 9: 2147 (2018) DOI: 10.1038/s41467-018-04587-w OA
Press release in EurekAlert
プレスリリース凝集したタンパク質を再生する分子機械ClpB の動的な構造変化の可視化に成功


47. Nakamura A, Tasaki T, Okuni Y, Song C, Murata K, Kozai T, Hara M, Sugimoto H, Suzuki K, Watanabe T, Uchihashi T, Noji H, *Iino R
Rate constants, processivity, and productive binding ratio of chitinase A revealed by single-molecule analysis
Phys Chem Chem Phys 2018 20: 3010-3018. DOI: 10.1039/C7CP04606E
Featured on the inside back cover!



46. #Baba M, #Iwamoto K, Iino R, Ueno H, Hara M, Nakanishia A, Kishikawa J, *Noji H, *Yokoyama K (#Equal contribution)
Rotation of artificial rotor axles in rotary molecular motors
Proc Natl Acd Sci USA 2016 113: 11214-11219. DOI: 10.1073/pnas.1605640113


45. Nakamura A, Tasaki T, Ishiwata D, Yamamoto M, Okuni Y, Visootsat A, Maximilien M, Noji H, Uchiyama T, Samejima M, Igarashi K, *Iino R
Single-molecule imaging analysis of binding, processive movement, and dissociation of cellobiohydrolase Trichoderma reesei Cel6A and its domains on crystalline cellulose
J Biol Chem 2016 291: 22404-22413. DOI: 10.1074/jbc.M116.752048
Featured on the cover!


44. #Isojima H, #Iino R, Niitani Y, Noji H, *Tomishige M (#Equal contribution)
Direct observation of intermediate states during the stepping motion of kinesin-1
Nat Chem Biol 2016 12: 290-297. DOI: 10.1038/nchembio.2028
News and Views in Nature Chemical Biology: Motor proteins: Kinesin's gait captured


43. *Matsumoto Y, Sakakihara S, Grushnikov A, Kikuchi K, Noji H, Yamaguchi A, Iino R, Yagi Y, Nishino K
A microfluidic channel method for rapid drug-susceptibility testing of Pseudomonas aeruginosa
PLOS ONE 2016. 11(2): e0148797. DOI: 10.1371/journal.pone.0148797



42. Obayashi Y, Iino R, *Noji H
A single-molecule digital enzyme assay using alkaline phosphatase with a cumarin-based fluorogenic substrate
Analyst 2015. 140: 5065-73. doi: 10.1039/c5an00714c


41. Enoki S, Iino R, Niitani Y, Minagawa Y, Tomishige M, *Noji H
High-speed angle-resolved imaging of single gold nanorod with microsecond temporal resolution and one-degree angle precision
Anal Chem 2015 87: 2079-2086. doi: 10.1021/ac502408c


40. Yukawa A, Iino R, Watanabe R, Hayashi S, *Noji H
Key chemical factors of arginine finger catalysis of F1-ATPase clarified by an unnatural amino acid mutation
Biochemistry 2015 54: 472–480. doi: 10.1021/bi501138b



39. #Ueno H, #Minagawa Y, Hara M, Rahman S, Yamato I, Muneyuki E, Noji H, *Murata T, *Iino R  (#Equal contribution)
Torque generation of Enterococcus hirae V-ATPase
J Biol Chem 2014 289: 31212-31223. doi: 10.1074/jbc.M114.598177


38. Ikeda T, Tsukahara T, Iino R, Takeuchi M, *Noji H
Motion capture and manipulation of single synthetic molecular rotors by optical microscopy
Angew Chem Int Ed 2014 53: 10082–10085. DOI: 10.1002/anie.201403091
プレスリリース: 1ナノメートルの人工分子マシン1個を「見て、触る」ことに成功:光学顕微鏡による 1分子モーションキャプチャ
Will be featured on the back cover!


37. Ikeda T, Iino R, *Noji H
Real-time fluorescence visualization of slow tautomerization of single free-base phthalocyanines under ambient conditions
Chem Commun 2014 50: 9443-9446. DOI: 10.1039/C4CC02574A
マイナビニュース記事. Introduced in UTokyo Research! (EnglishJapanese)
Real-time visualization of slow tautomerization in a single organic chromophore : Candidate for a 1-nanometer-sized molecular memory
Featured on the front cover!


36. Shibafuji Y, Nakamura A, Uchihashi T, Sugimoto N, Fukuda S, Watanabe H, Samejima M, Ando T, Noji H, Koivula A, Igarashi K, *Iino R
Single-molecule imaging analysis of elementary reaction steps of Trichoderma reesei cellobiohydrolase I (Cel7A) hydrolyzing crystalline cellulose Iα and IIII
J Biol Chem 2014 289: 14056-14065. doi: 10.1074/jbc.M113.546085


35. Takehara H, Miyazawa K, Noda T, Sasagawa K, Tokuda T, Kim SH, Iino R, Noji H, *Ohta J
A CMOS image sensor with stacked photodiodes for lensless observation system of digital enzyme-linked immunosorbent assay
Jpn J Appl Phys 2014 53: 04EL02. doi: 10.7567/JJAP.53.04EL02



34. #Minagawa Y, #Ueno H, Hara M, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Yamato I, Muneyuki E, Noji H, *Murata T, *Iino R (#Equal contribution)
Basic properties of rotary dynamics of the molecular motor Enterococcus hirae V1-ATPase
J Biol Chem 2013 288: 32700-32707. doi: 10.1074/jbc.M113.506329
Featured on the front cover! Designed by SCIEMENT


33. Fukuda S, Uchihashi T, Iino R, Okazaki Y, Yoshida M, Igarashi K, and *Ando T
High-speed atomic force microscope combined with single-molecule fluorescence microscope
Rev Sci Instrum 2013 84: 073706. doi: 10.1063/1.4813280


32. Watanabe R, Tabata KV, Iino R, Ueno H, Iwamoto M, Oiki S, *Noji H
Biased Brownian stepping rotation of FoF1-ATP synthase driven by proton motive force
Nat Commun 2013 4: 1631. DOI:10.1038/ncomms2631



31. Enoki S, Iino R, Morone N, Kaihatsu K, Sakakihara S, Kato N, *Noji H
Label-free single-particle imaging of the influenza virus by objective-type total internal reflection dark-field microscopy
PLOS ONE 2012. 7: e49208. DOI:10.1371/journal.pone.0049208.


30. Kim SH, Iwai S, Araki S, Sakakihara S, Iino R, *Noji H
Large-scale femtoliter droplet array for digital counting of single biomolecules
Lab Chip 2012. 12: 4986-4991. DOI: 10.1039/C2LC40632B


29. You H, Iino R, Watanabe R, *Noji H.
Winding single-molecule double-stranded DNA on a nanometer-sized reel
Nucleic Acids Research 2012. 40: e151. doi: 10.1093/nar/gks651


28. *Iino R, Hayama K, Amezawa H, Sakakihara S, Kim SH, Matsumoto Y, Nishino K, Yamaguchi A, Noji H.
A single-cell drug efflux assay in bacteria by using a directly accessible femtoliter droplet array
Lab Chip 2012. 12: 3923-3929. DOI: 10.1039/C2LC40394C
Introduced as one of the Emerging Investigators in Lab on a Chip!


27. *Hayashi S, Ueno H, Shaikh AR, Umemura M, Kamiya M, Ito Y, Ikeguchi M, Komoriya Y, Iino R, Noji H.
Molecular mechanism of ATP hydrolysis in F1-ATPase revealed by molecular simulations and single molecule observations
J Am Chem Soc 2012. 134: 8447–8454. DOI:10.1021/ja211027m


26. Komoriya Y, Ariga T, Iino R, Imamura H, Okuno D, *Noji H.
Principle role of the arginine finger in rotary catalysis of F1-ATPase
J Biol Chem 2012. 287: 15134-15142. DOI: 10.1074/jbc.M111.328153


25. *Sasagawa K, Ando K, Kobayashi T, Noda T, Tokuda T, Kim SH, Iino R, Noji H, Ohta J.
Complementary metal–oxide–semiconductor image sensor with microchamber array for fluorescent bead counting
Jpn J Appl Phys 2012. 51. 02BL0. DOI: 10.1143/JJAP.51.02BL01


24. #Watanabe R, #Okuno D, Sakakihara S, Shimabukuro K, Iino R, Yoshida M, *Noji H. (#Equal contribution)
Mechanical modulation of catalytic power on F1-ATPase
Nat Chem Biol 2012. 8: 86-92. doi:10.1038/nchembio.715



23. #Uchihashi T, #Iino R, *Ando T, *Noji H. (#Equal contribution)
High-speed atomic force microscopy reveals rotary catalysis of rotorless F1-ATPase
Science 2011. 333: 755-758. DOI: 10.1126/science.1205510
Perspective of the Science
News of the Chemistry World
Research Highlight of the Nature Nanotech.
News of the BioTechniques



22. *Matsumoto Y, Hayama K, Sakakihara S, Nishino K, Noji H, *Iino R, Yamaguchi A.
Evaluation of multidrug efflux pump inhibitors by a new method using microfluidic channels
PLOS ONE 2011.  6: e18547.



21. Okuno D, Iino R, and *Noji H.
Stiffness of γ subunit of F1-ATPase
Eur Biophys J 2010. 39:1589-1596.


20. Watanabe R, Iino R, *Noji H.
Phosphate-release in F1-ATPase catalytic cycle follows ADP release
Nat Chem Biol 2010. 6: 814–820. doi:10.1038/nchembio.443

Introduced in News and Views!


19. *Hayashi K, Ueno H, Iino R, and *Noji H.
Fluctuation theorem applied to F1-ATPase
Phys Rev Lett 2010. 104: 218103-1-218103-4.


18. Ueno H, Nishikawa S, Iino R, Tabata KV, Sakakihara S, Yanagida T, *Noji H.
Simple dark-field microscopy with nanometer spatial precision and microsecond temporal resolution
Biophys J 2010. 98: 2014-2023.


17. Saita E, Iino R, Suzuki T, Feniouk BA, Kinosita K. Jr, *Yoshida M.
Activation and stiffness of the inhibited states of F1-ATPase probed by single-molecule manipulation
J Biol Chem 2010. 285: 11411-11417.


16. Sakakihara S, Araki S, *Iino R, *Noji H.
A single-molecule enzymatic assay in a directly accessible femtoliter droplet array
Lab Chip 2010. 10: 3355-3362.



15. *Imamura H, Huynh Nhat KP, Togawa H, Saito K, Iino R, Kato-Yamada Y, Nagai,T, *Noji H.
Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators
Proc Natl Acad Sci USA 2009. 106: 15651-15656.


14. Enoki S, Watanabe R, Iino R, and *Noji H.
Single-molecule study on the temperature-sensitive reaction of F1-ATPase with a hybrid F1 carrying a single β(E190D)
J Biol Chem 2009. 284: 23169-23176.


13. *Iino R, Hasegawa R, Tabata KV, *Noji H.
Mechanism of inhibition by C-terminal α-helices of the ε subunit of Escherichia coli FoF1-ATP synthase
J Biol Chem 2009. 284:17457-17464.



12. Okuno D, Fujisawa R, Iino R, Hirono-Hara Y, Imamura H, *Noji H.
Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation
Proc Natl Acad Sci USA 2008. 105: 20722-20727.


11. Watanabe R, Iino R, Shimabukuro K, Yoshida M, *Noji H.
Temperature-sensitive reaction intermediate of F1-ATPase
EMBO rep 2008. 9: 84-90.



10. Suzuki KGN, Fujiwara TK, Sanematsu F, Iino R, Edidin M, and *Kusumi A.
GPI-anchored receptor clusters transiently recruit Lyn and Gα for temporary cluster immobilization and Lyn activation: single-molecule tracking study 1
J Cell Biol 2007. 177: 717-730.



9. Iino R, Murakami T, Iizuka S, Kato-Yamada Y, Suzuki T and *Yoshida M.
Real-time monitoring of conformational dynamics of the epsilon subunit in F1-ATPase
J Biol Chem 2005. 280: 40130-40134.


8. Makiyo H, Iino R, Ikeda C, Imamura H, Tamakoshi M, Iwata M, Stock D, Bernal RA, Carpenter EP, Yoshida M, *Yokoyama K and *Iwata S.
Structure of a central stalk subunit F of Prokaryotic V-type ATPase/synthase from Thermus thermophilus
EMBO J 2005. 24: 3974-3983.


7. Koyama-Honda I, Ritchie K, Fujiwara T, Iino R, Murakoshi H, Kasai RS, and *Kusumi A.
Fluorescence imaging for monitoring the colocalization of two single molecules in living cells
Biophys J 2005. 88: 2126-2136.



6. Murase K, Fujiwara T, Umemura Y, Suzuki K, Iino R, Yamashita H, Saito M, Murakoshi H, Ritchie K, and *Kusumi A.
Ultrafine membrane Compartments for molecular diffusion as revealed by single molecule techniques
Biophys J 2004. 86: 4075-4093.


5. Murakoshi H, Iino R, Kobayashi T, Fujiwara T, Ohshima C, Yoshimura A, and *Kusumi A.
Single-molecule imaging analysis of ras activation in living cells
Proc Natl Acad Sci USA 2004. 101: 7317-7322.



4. Suzuki T, Murakami T, Iino R, Suzuki J, Ono S, Shirakihara Y, and *Yoshida M.
FoF1-ATPase/synthase is geared to the synthesis mode by conformational rearrangement of epsilon subunit in response to proton motive force and ADP/ATP balance
J Biol Chem 2003. 278: 46840-46846.


3. Nakada C., Ritchie K., Oba Y, Nakamura M, Hotta Y, Iino R, Kasai S, Yamaguchi K, Fujiwara T, and *Kusumi A.
Accumulation of anchored proteins forms membrane diffusion barriers during neuronal polarization
Nat Cell Biol 2003. 5: 626-632.


2. Ike H, Kosugi A, Kato A, Iino R, Hirano H, Fujiwara T, Ritchie K, and *Kusumi A.
Mechanism of Lck recruitment to the T-cell receptor cluster as studied by single molecule fluorescence video imaging
ChemPhysChem 2003. 4: 620-626.



1. Iino R, Koyama I, and *Kusumi A.
Single molecule imaging of green fluorescent protein in living cells: E-cadherin forms oligomers on the free cell surface
Biophys J 2001. 80: 2667-2677.