Grant‐in‐Aid for Scientific Research on Innovative Areas
(Research in a proposed research area)

Novel measurement techniques forvisualizing 'live' protein molecules at work

Achivements

The number of research papers published every year
5 in 2014 / 56 in 2015 / 82 in 2016 / 63 in 2017 / 84 in 2018 / 45 in 2019
335 in Total

Papers in 2018

1.
*Kohda D.
"Multiple partial recognitions in dynamic equilibrium" in the binding sites of proteins form the molecular basis of promiscuous recognition of structurally diverse ligands.
Biophys Rev 10 , 421-433 (2018)
2.
*Kohda D.
Structural basis of protein Asn-glycosylation by oligosaccharyltransferase.
Adv Exp Med Biol 1104 , 171-199 (2018)
3.
Srivastava A, Tama F, Kohda D, *Miyashita O.
Computational investigation of the conformational dynamics in Tom20-mitochondrial presequence tethered complexes.
Proteins 87 , 81-90 (2018)
4.
Fujinami D, -Mahin AA, Elsayed KM, Islam MR, Nagao JI, Roy U, Momin S, Zendo T, *Kohda D, *Sonomoto K.
The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states.
Commun Biol 1 , 150 (2018)
5.
Brouns T, De. Keersmaecker H, Konrad S, Kodera N, Ando T, Lipfert J, De Feyter S, *Vanderlinden W.
Free energy landscape and dynamics of supercoiled DNA by high-speed atomic force microscopy,
ACS Nano 12 , 11907–11916 (2018)
6.
Mori T, Sugiyama S, Byme M, Johnson CH, Uchihashi T, *Ando T.
Revealing circadian mechanisms of integration and resilience by visualizing clock proteins working in real time.
Nat Commun 9 , 3245 (2018)
7.
Ando T et al.
Topical Review: The 2018 correlative microscopy techniques roadmap.
J Phys D Appl Phys 51 , 443001 (42pages) (2018)
8.
Uchihashi T, Watanabe Y, Nakazaki Y, Yamasaki T, Watanabe H, Maruno T, Ishii K, Uchiyama S, Song C, Murata K, Iino R, *Ando T.
Dynamic structural states of ClpB involved in its disaggregation function.
Nat Commun 9 , 2147 (2018)
9.
Ravula T, Ishikuro D, Kodera N, Ando T, Anantharamaiah G, Ramamoorthy A.
Real time monitoring of lipid exchange via fusion of peptide based lipid-nanodiscs.
Chem. Mater 30 , 3204-3207 (2018)
10.
Umakoshi T, Udaka H, Uchihashi T, Ando T, Suzuki M, *Fukuda T.
Quantum-dot antibody conjugation visualized at the single-molecule scale with high-speed atomic force microscopy.
Colloid Surf B, Biointerfaces 167 , 267-274 (2018)
11.
Terahara N, Inoue Y, Kodera N, Morimoto YV, Uchihashi T, Imada K, Ando T, *Namba K, *Minamino T.
Insight into structural remodeling of the FlhA ring responsible for bacterial flagellar type III protein export.
Sci Adv 4 , eaao7054 (2018)
12.
Haruyama T, Uchihashi T, Yamada Y, Kodera N, *Ando T, *Konno H.
Negatively charged lipids are essential for functional and structural switch of human 2-Cys peroxiredoxin II.
J Mol Biol 430 , 602-610 (2018)
13.
Takeda T, Kozai T, Yang H, Ishikuro D, Seyama K, Kumagai Y, Abe T, Yamada H, Uchihashi T, *Ando T, *Takei K.
Dynamic clustering of dynamin-amphiphysin helices regulates membrane constriction and fission coupled with GTP hydrolysis.
e-Life 7 , e30246 (2018)
14.
*Ando T.
High-speed atomic force microscopy and its future prospects.
Biophys Rev 10 , 285–292 (2018)
15.
Kawagoe S, Nakagawa H, Kumeta H, *Ishimori K, *Saio T.
Structural insight into proline cis/trans isomerization of unfolded proteins catalyzed by the trigger factor chaperone.
J Biol Chem 293 , 15095-15106 (2018)
16.
Saio T, Kawagoe S, Ishimori K, Kalodimos CG.
Oligomerization of a molecular chaperone modulates its activity.
Elife 7 , e35731 (2018)
17.
Sato W, Uchida T, Saio T, Ishimori K.
Polyethylene glycol promotes autoxidation of cytochrome c.
Biochim Biophys Acta Gen Subj 1862 , 1339-1349 (2018)
18.
O'Brien H, Kanemura S, Okumura M, Baskin P, Bandyopadhyay P, Ellgaard L, Inaba K, *Safavi-Hemami H.
Ero1-mediated reoxidation of PDI accelerates the folding of cone-snail toxins
Int J Mol Sci 11 , E3418 (2018)
19.
Kinoshita M, Lin Y, Itoh D, Okumura M, Markova N, Ladbury JE, Sterpone F, *Lee YH.
Energy landscape of polymorphic amyloid generation of β2-microglobulin revealed by calorimetry,
Chem Commun (Camb) 57 , 7995-7998 (2018)
20.
Terakawa MS, Lin Y, Kinoshita M, Kanemura S, Itoh D, Sugiki T, Okumura M, Ramamoorthy A, *Lee YH.
Impact of membrane curvature on amyloid aggregation,
Biochim Biophys Acta Biomembr 1860 , 1741-1764 (2018)
21.
Arai K, Takei T, Shinozaki R, Noguchi N, Fujisawa S, Katayama H, Moroder L, Ando S, Okumura M, Inaba K, *Hojo H, *Iwaoka M.
Characterization and optimization of two-chain folding pathways of insulin via native chain assembly.
Communications Chemistry 1 , e26 (2018)
22.
Lin MI, Hiyama A, Kondo K, *Nagata T, *Katahira M.
Classification of fungal glucuronoyl esterases (FGEs), and characterization of two new FGEs from Ceriporiopsis subvermispora and Pleurotus eryngii.
Appl Microbiol Biotechnol 102 , 9635-9645 (2018)
23.
Lin MI, *Nagata T, *Katahira M.
High yield production of fungal manganese peroxidases by E. coli through soluble expression, and examination of the activities.
Prot Exp Purif 145 , 45-52 (2018)
24.
Wan OWH, Mikami B, Saka N, Kondo K, Lin MI, *Nagata T, *Katahira M.
Characterization of the glutathione S-transferases that belong to the GSTFuA class in Ceriporiopsis subvermispora: Implications in intracellular detoxification and metabolism of wood-derived compounds.
Int J Biol Macromol 113 , 1158-1166 (2018)
25.
Nakajima Y, Umena Y, Nagao R, Endo K, Kobayashi K, Akita F, Suga M, Wada H, Noguchi T, and *Shen JR.
Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II in thermosynechococcus elongatus.
J Biol Chem 293 , 14786-14797 (2018)
26.
*Kato Y, Akita F, Nakajima Y, Suga M, Umena Y, Shen JR, and *Noguchi T.
Fourier transform infrared analysis of the S-state cycle of water oxydation in the microcrystals of photosystem II.
J Phys Chem Lett 9 , 2121-2126 (2018)
27.
Okuno, D., Hirano, M., Yokota, H., Ichinose, J., Kira, T., Hijiya, T., Uozumi, C., Yamakami, M., *Ide, T.
A gold nano-electrode for single ion channel recordings.
Nanoscale 10 , 4036-4040 (2018)
28.
Yamaguchi M, Satoo K, Suzuki H, Fujioka Y , Ohsumi Y, Inagaki F, *Noda NN.
Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition.
J Mol Biol 430 , 249-257 (2018)
29.
Nishikino T, Hijikata A, Miyanoiri Y , Onoue Y, Kojima S, Shirai T, *Homma, M.
Rotational direction of flagellar motor from the conformation of FliG middle domain in marine Vibrio.
Sci Rep 8 , 17793 (2018)
30.
Yoshida H, Tanimoto E, Hirai T, Miyanoiri Y, Mitani R, Kawamura M, Takeda M, Takehara S, Hirano K, Kainosho M, Akagi T, Matsuoka M, *Ueguchi-Tanaka M.
Evolution and diversification of the plant gibberellin receptor GID1.
Proc. Natl. Acad. Sci. U.S.A. 115 , E7844-53 (2018)
31.
*Kainosho M, Miyanoiri Y, Terauchi T, Takeda M.
Perspective: next generation isotope-aided methods for protein NMR spectroscopy.
J Biomol NMR 71 , 119-27 (2018)
32.
*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)
33.
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.
Physical Chemistry Chemical Physics 20 , 3010-3018 (2018)
34.
Terada, D., Sotoma, S., Harada, Y., *Igarashi, R and *Shirakawa, M.
One-Pot Synthesis of Highly Dispersible Fluorescent Nanodiamonds for Bioconjugation.
Bioconj Chem 29 , 2786-2792(2018)
35.
Fujita, H., Tokunaga, A., Shimizu, S., Whiting, A.L., Aguilar-Alonso, F., Takagi, K., Walinda, E., Sasaki, Y., Shimokawa, T., Mizushima, T., Ohki, I., Ariyoshi, M., Tochio, H., Bernal, F., Shirakawa, M. , and *Iwai, K.
Cooperative domain formation by homologous motifs in HOIL-1L and SHARPIN plays crucial roles in LUBAC stabilization.
Cell Rep 23 , 1192-1204(2018)
36.
Shingo Sotoma, Daiki Terada, Takuya F. Segawa, Ryuji Igarashi* Yoshie Harada* Masahiro Shirakawa*,
Enrichment of ODMR-active nitrogen-vacancy centres in five-nanometre-sized detonation-synthesized nanodiamonds: Nanoprobes for temperature, angle and position.
Sci Rep 8 , 5463(2018)
37.
Morimoto D, Walinda E, Shinke M, Sugase K, *Shirakawa M, 
Isolation and characterization of a minimal building block of polyubiquitin fibrils.
Sci Rep 8 , 2711(2018)
38.
Mochizuki A, Saso A, Zhao Q, Kubo S, *Nishida N, *Shimada I.
Balanced Regulation of Redox Status of Intracellular Thioredoxin Revealed by in-Cell NMR.
J Am Chem Soc 140 , 3784-3790 (2018)
39.
Yoshida H, Tanimoto E, Hirai T, Miyanoiri Y, Mitani R, Kawamura M, Takeda M, Takehara S, Hirano K, Kainosho M, Akagi T, Matsuoka M, *Ueguchi-Tanaka M.
Evolution and diversification of the plant gibberellin receptor GID1.
Proc Natl Acad Sci U S A 115 , E7844-E7853 (2018)
40.
*Kainosho M, Miyanoiri Y, Terauchi T, Takeda M.
Perspective: next generation isotope-aided methods for protein NMR spectroscopy.
J Biomol NMR 71 , 119-127 (2018)
41.
Colaluca IN, Basile A, Freiburger L, D'Uva V, Disalvatore D, Vecchi M, Confalonieri S, Tosoni D, Cecatiello V, Malabarba MG, Yang CJ, Kainosho M, Sattler M, Mapelli M, Pece S, *Di Fiore PP.
A Numb-Mdm2 fuzzy complex reveals an isoform-specific involvement of Numb in breast cancer.
J Cell Biol 217 , 745-762 (2018)
42.
Murakami, M., Kano, F., *Murata, M.
LLO-mediated cell resealing system for analyzing intracellular activity of membrane-impermeable biopharmaceuticals of mid-sized molecular weight
Sci Rep 8 , 1946 (2018)
43.
*Watanabe, R., Komatsu, T., Sakamoto, S., *Noji, H.
High-throughput single-molecule bioassay using micro-reactor arrays with a concentration gradient of target molecules.
Lab on a Chip 18 , 2849-2853 (2018)
44.
*Watanabe, R., Sakuragi, T., *Noji, H., *Nagata, S.
Single molecule analysis of phospholipid scrambling by TMEM16F.
Proc Natl Acad Sci USA 115 , 3066-3071 (2018)
45.
*Watanabe, R., Soga, N., Ohdate, S., *Noji, H.
Single molecule analysis of membrane transporter activity by using a microsystem.
Methods in Molecular Biology 1700 , 321-330 (2018)
46.
*Ikeya T, *Ito Y,
Protein NMR structure refinement based on Bayesian Inference for dynamical ordering of biomacromolecules.
J Comput Chem Jpn 17 , 65-75 (2018)
47.
*Ikeya T, Ban D, Lee D, Ito Y, Kato K, *Griesinger C.
Solution NMR views of dynamical ordering of biomacromolecules.
Biochim Biophys Acta Gen Subj 1862 , 287-306 (2018)
48.
Negishi H, *Abe S, Yamashita K, Hirata K, Niwase K, Boudes M, Coulibaly F, Mori H, *Ueno T.
Supramolecular protein cages constructed from a crystalline protein matrix.
Chem Commun 54 , 1988-1991 (2018)
49.
*Abe S, Atsumi K, Yamashita K, Hirata K, Mori H, *Ueno T.
Structure of in cell protein crystals containing organometallic complexes.
Phys Chem Chem Phys 20 , 2986-2989 (2018)
50.
Kobayashi N, Hattori Y, Nagata T, Shinya S, Güntert P, Kojima C, *Fujiwara T.
Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks.
Bioinformatics 34 , 4300-4301 (2018)
51.
Hattori Y, Yamanaka D, Morioka S, Yamaguchi T, Tomonari H, Kojima C, *Tanaka Y.
NMR spectroscopic characterization of a model RNA duplex reflecting the core sequence of hammerhead ribozymes.
Nucleos Nucleot Nucleic Acids 37 , 383-396 (2018)
52.
Sugiki T, Egawa D, Kumagai K, Kojima C, Fujiwara T, Takeuchi K, Shimada I, *Hanada K, *Takahashi H.
Phosphoinositide binding by the PH domain in ceramide transfer protein (CERT) is inhibited by hyperphosphorylation of an adjacent serine-repeat motif.
J Biol Chem 293 , 11206-11217 (2018)
53.
Sugiki T, Furuita K, Fujiwara T, *Kojima C,
Amino acid selective 13C-labeling and 13C-scrambling profile analysis of protein alpha and side-chain carbons in E. coli utilized for protein NMR.
Biochemistry
57 , 3576-3589 (2018)
54.
*Kojima S, Takao M, Almira G, Kawahara I, Sakuma M, Homma M, *Kojima C, *Imada K.
The helix rearrangement in the periplasmic domain of the flagellar stator B-subunit activates peptidoglycan binding and ion influx.
Structure 26 , 590-598 (2018)
55.
Kaneko-Suzuki M, Ishikawa R, Terakawa C, Kojima C, Fujiwara M, Ohki I, Tsuji H, Shimamoto K, *Taoka K.
TFL1-like proteins in rice antagonize rice FT-like protein in inflorescence development by competition for complex formation with 14-3-3 and FD.
Plant Cell Physiol 59 , 458-468 (2018)
56.
Lim SK, *Wong RW
Targeting nucleoporin POM121-importin β axis in prostate cancer.
Cell Chem Biol 25 , 1056-1058 (2018)
57.
Dewi FRP, Domoto T, Hazawa M, Kobayashi A, Douwaki T, Minamoto T and *Wong RW,
Colorectal cancer cells require glycogen synthase kinase-3β for sustaining mitosis via translocated promoter region (TPR)-dynein interaction.
Oncotarget 9 , 13337-13352 (2018)
58.
Hazawa M, Lin D, Kobayashi A, Jiang YY, Dewi FRP, Mohamed MS, Hartono H, Nakada S, Meguro-Horike M, Horike S, Koeffler H and *Wong RW,
Rock-dependent phosphorylation of NUP62 regulates p63 nuclear transport and cell fate of squamous cell carcinoma.
EMBO Rep 19 , 73-88 (2018)
59.
Miyazaki R, Myogo N, Mori H, *Akiyama Y,
A new photo-cross-linking approach for analysis of protein dynamics in vivo.
J Biol Chem 293 , 677-686 (2018)
60.
*Mori H, Sakashita S, Ito J, Ishii E, Akiyama Y.
Identification and characterization of arrest motif in VemP by systematic mutational analysis.
J Biol Chem 293 , 2915-2926 (2018)
61.
*Takiguchi K, Hayashi M, Kazayama Y, Toyota T, Harada Y, Nishiyama M.
Morphological Control of Microtubule-Encapsulating Giant Vesicles by Changing Hydrostatic Pressure.
Biological & Pharmaceutical Bulletin 41 , 288-293 (2018)
62.
Fujii S, Masanari FM、Kobayashi S, Kato C, Nishiyama M, Harada Y, Wakai S, Sambongi Y.
Commonly stabilized cytochromes c from deep-sea Shewanella and Pseudomonas.
Bioscience, Biotechnology, and Biochemistry 82 , 792-799 (2018)
63.
*Nishiyama M.
Controlling the Motility of ATP-Driven Molecular Motors Using High Hydrostatic Pressure.
The Role of Water in ATP Hydrolysis. Springer, Singapore , pp 325-337 (2018)
64.
Matsunaga Y, Sugita Y,
Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning.
eLife 7 , e32668 (2018)
65.
Matsunaga Y, Sugita Y,
Refining Markov State Models for conformational dynamics using ensemble-averaged data and time-series trajectories.
J Chem Phys 148 , 241731 (2018)
66.
Kamiya M, Sugita Y,
Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations.
J Chem Phys 149 , 072304 (2018)
67.
Tanaka Y, Izumioka A, Abdul HA, Fujii A, Haruyama T, Furukawa A and *Tsukazaki T. .
2.8-Å crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop.
Biochem. Biophys. Res. Commun. 505 , 141-145 (2018)
68.
*Tsukazaki T. .
Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor.
FEMS Microbiology Letters 365 , 112 (2018)
69.
Furukawa A, Nakayama S, Yoshikaie K, Tanaka Y and *Tsukazaki T. .
Remote Coupled Drastic β-Barrel to β-Sheet Transition of the Protein Translocation Motor.
Structure 26 , 485–489 (2018)
70.
Takazaki Hiroko, Hirofumi Shimizu, Takuo Yasunaga.
Structural Analysis of KcsA by Cryo-EM Single Particle Analysis.
Microscopy 67 (suppl_2) , i35 (2018)
71.
Maki-Yonekura S, Matsuoka R, Yamashita Y, Shimizu H, Tanaka M, Iwabuki F, Yonekura K.
Hexameric and pentameric complexes of the ExbBD energizer in the Ton system.
eLife 7 , E35419 (2018)
72.
Kimura T, Lorenz-Fonfria VA, Douki S, Motoki H, Ishitani R, Nureki O, Higashi M, *Furutani Y.
Vibrational and molecular properties of Mg2+ binding and selectivity in the magnesium channel MgtE.
J Phys Chem B 122 , 9681-9696 (2018)
73.
Komiya R, Kimura T, Nomura T, Kubo M, *Yan J.
Ultraprecision cutting of single-crystal calcium fluoride for fabricating micro flow cells.
J Adv Mech Design Sys, and Manuf 12 , JAMDSM0021 (2018)
74.
Kobayashi A, Takayama Y, Okajima K, Oide M, Yamamoto T, Sekiguchi Y, Oroguchi T, *Nakasako M, Kohmura Y, Yamamoto M, Hoshi T, Torizuka Y.
Diffraction apparatus and procedure in tomography X-ray diffraction imaging for biological cells at cryogenic temperature using synchrotron X-ray radiation.
J Synchrotron Rad 25 , 1803-1818 (2018)
75.
Oroguchi T, Yoshidome T, Yamamoto T, *Nakasako M.
Growth of cuprous oxide particles in liquid-phase synthesis investigated by X-ray laser diffraction.
Nano Lett 18 , 5192-5197 (2018)
76.
Oide M, Sekiguchi Y, Fukuda A, Okajima K, Oroguchi T, *Nakasako M.
Classification of ab initio models of proteins restored from small-angle X-ray scattering.
J Synchrotron Rad 25 , 1379-1388 (2018)
77.
Kobayashi A, Sekiguchi Y, Oroguchi T, Yamamoto M, *Nakasako M.
Shot-by-shot characterization of focused X-ray fr,lectron laser pulses.
Scientific Reports 8 , 831 (2018)
78.
Oide M, *Okajima K, Nakagami H, Kato T, Sekiguchi Y, Oroguchi T, Hikima T, Yamamoto M, *Nakasako M.
Blue-light excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis.
J Biol Chem 293 , 963–972 (2018)
79.
Yagi-Utsumi, M., Sikdar, A., Kozai, T., Inoue, R., Sugiyama, M., Uchihashi, T., Yagi, H. , Satoh, T., *Kato K.
Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation.
Protein Engineering, Design and Selection 31 , 29-36. (2018)
80.
*Brinson RG, Marino JP, Delaglio F, Arbogast LW, Evans RM, Kearsley A, Gingras G, Ghasriani H, Aubin Y, Pierens GK, Jia X, Mobli M, Grant HG, Keizer DW, Schweimer K, StÅhle J, Widmalm G, Zartler ER, Lawrence CW, Reardon PN, Cort JR, Xu P, Ni F, Yanaka S, Kato K, Parnham SR, Tsao D, Blomgren A, RundlÖf T, Trieloff N, Schmieder P, Ross A, Skidmore K, Chen K, Keire D, Freedberg DI, Suter-Stahel T, Wider G, Ilc G, Plavec J, Bradley SA, Baldisseri DM, SforÇa ML, Zeri ACM, Wei JY, Szabo CM, Amezcua CA, Jordan JB, WikstrÖm M,
Enabling adoption of 2D-NMR for the higher order structure assessment of monoclonal antibody therapeutics,
mAbs 11 , 94-105 (2018)
81.
Yagi H, Yanaka S, *K. Kato,
Structure and Dynamics of Immunoglobulin G Glycoproteins
Advances in experimental medicine and biology 1104 , 219-235 (2018)
82.
Yanaka S, Yagi H, Yogo R, Yagi-Utsumi M, *Kato K.
Stable isotope labeling approaches for NMR characterization of glycoproteins using eukaryotic expression systems.
J Biomol NMR 71 , 192-202 (2018)
83.
Yogo R, Yanaka S, *Kato K.
Backbone 1H, 13C, and 15N assignments of the extracellular region of human Fcγ receptor IIIb.
Biomol. NMR Assign 12 , 201-204 (2018)
84.
*Kato K, Yanaka S, Yagi H.
Technical basis for nuclear magnetic resonance approach for glycoproteins
In: Experimental approaches of NMR spectroscopy-Methodology and application to life science and materials science- Springer (Singapore) , pp415-438 (2018)


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