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

Novel measurement techniques forvisualizing 'live' protein molecules at work


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 2019

Yamasaki T, *Kohda D.
A Radioisotope-free Oligosaccharyltransferase Assay Method.
Bio-protocol 9 , e3186 (2019)
Umakoshi T, Fukuda S, Iino R, Uchihashi T, *Ando T.
High-speed near-field fluorescence microscopy combined with high-speed atomic force microscopy for biological studies.
BBA-Gen Subj , in press
Inoue Y, Ogawa Y, Kinoshita M, Terahara N, Shimada M, Kodera N, Ando T, Namba K, *Kitao A, *Imada K, *Minamino T.
Structural insights into the substrate specificity switch mechanism of the type III protein export apparatus.
Structure , in press
Lim KS, Mohamed MS, Wang H, Hartono, Hazawa M, Kobayashi A, Voon DCC, Kodera N, Ando T, Wong RW.
Direct visualization of avian influenza H5N1 Hemagglutinin precursor and its conformational change by high-speed atomic force microscopy.
BBA- Gen Subj , in press
Sahoo BR, Genjo T, Watanabe-Nakayama T, Stoddard AK, Ando T, Yasuhara K, Fierke CA, *Ramamoorthy A.
Cationic polymethacrylate-copolymer acts as an agonist for β-amyloid and antagonist for amylin fibrillation.
Chem Sci 10 , 3976-3986 (2019)
Owa M, Uchihashi T, Yanagisawa H, Yamano T, Iguchi H, Fukuzawa H, Wakabayashi K, Ando T, *Kikkawa M.
Inner lumen proteins stabilize doublet microtubules in cilia and flagella.
Nat Commun 10 , 1143 (2019)
Maruyama S, Suzuki K, Imamura M, Sasaki H, Matsunami H, Mizutani K, Saito Y, Imai FL, Ishizuka-Katsura Y, Kimura-Someya T, Shirouzu M, Uchihashi T, Ando T, Yamato I, *Murata T.
Metastable asymmetrical structure of shaftless V1 motor.
Sci Adv 5 , eaau8149 (2019)
Kori S, Ferr yL, Matano S, Jimenji T, Kodera N, Tsusaka T, Matsumura R, Oda T, Sato M, Dohmae N, Ando T, Shinkai Y, Defossez PA, *Arita K.
Structure of the UHRF1 Tandem Tudor Domain bound to a methylated non-histone protein, LIG1, reveals rules for binding and regulation.
Structure 27 , 485-496 (2019)
Sone E, Noshiro D, Ikebuchi Y, Nakagawa M, Khan M, Tamura Y, Ikeda M, Oki M, Murali R, Fujimori T, Yoda T, Honma M, Suzuki H, Ando T, *Aoki K.
The clustering-induction of RANKL molecules could stimulate early osteroblast differentiation.
Biophys Biochem Res Commun 509 , 435-440 (2019)
Haruyama T, Sugano Y, Kodera N, Uchihashi T, Ando T, Tanaka Y, Konno H, *Tsukazaki T.
Single-unit imaging of membrane protein-embedded nanodiscs from two oriented sides by high-speed atomic force microscopy.
Structure 27 , 152-160 (2019)
*Okumura M, Noi K, Kanemura S, Kinoshita M, Saio T, Inoue Y, Hikima T, Akiyama S, *Ogura T, *Inaba K.
Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding.
Nat Chem Biol 15 , 499-509 (2019)
*Saio T, Ishimori K.
Accelerating structural life science by paramagnetic lanthanide probe methods.
Biochim Biophys Acta Gen Subj , in press (2019)
*Okumura M, Noi K, Kanemura S, Kinoshita M, Saio T, Inoue Y, Hikima T, Akiyama S, *Ogura T, *Inaba K.
Dynamic assembly of protein disulfide isomerase in catalysis of oxidative protein folding,
Nature Chemical Biology 15 , 499-509 (2019)
Matsusaki M, Kanemura S, Kinoshita M, Lee YH, *Inaba K, *Okumura M.
Protein Disulfide Isomerase family: from Proteostasis to Pathogenesis,
Biochim Biophys Acta-general subjects , in press (2019)
Okada S, Matsusaki M, Arai K, Hidaka Y, Inaba K, *Okumura M, *Muraoka T.
Coupling effects of thiol and urea-type groups for promotion of oxidative protein folding,
Chem Commun (Camb) 55 , 759-762 (2019)
Wan L, Kanba K, *Nagata T, *Katahira M.
An insight into the dependence of the deaminase rate of human APOBEC3F on the length of single-stranded DNA, which is affected by the concentrations of APOBEC3F and single-stranded DNA.
Biochim Biophys Acta General Subject , in press (2019)
Iida M, Mashima T, Yamaoki Y, So M, Nagata T, *Katahira M.
The anti-prion RNA aptamer R12 disrupts the Alzheimer’s disease-related complex between prion and amyloid.
FEBS J , in press (2019)
Wan OWH, Mikami B, Saka N, Kondo K, Lin MI, *Nagata T, *Katahira M.
Identification of key residues for activities of atypical glutathione S-transferase of Ceriporiopsis subvermispora, a selective degrader of lignin in woody biomass, by crystallography and functional mutagenesis.
Macromol 132 , 222-229 (2019)
Wan OWH, Mikami B, Saka N, Kondo K, Lin MI, *Nagata T, *Katahira M.
Structure of a serine-type glutathione S-transferase of Ceriporiopsis subvermispora and identification of the enzymatically important non-canonical residues by functional mutagenesis.
Biochem Biophys Re. Commun 510 , 177-183 (2019)
Wang W, Yu L, Xu C, Tomizaki T, Zhao S, Umena Y, Chen X, Qin X, Xin Y, Suga M, Hang G, Kuang T, and *Shen JR.
Structural basis for blue-green light harvesting and energy dissipation in diatoms.
Science 363 , eaav0365 (2019)
*Yokota, H
Fluorescence microscopy for visualizing single-molecule protein dynamics.
Bicohim. Biophys. Acta Gen. Subj , in press (2019)
Iwakawa N, Mahana Y, Ono A, Ohki I, Walinda E, Morimoto D, Sugase K, *Shirakawa M.
Backbone and side-chain resonance assignments of the methyl-CpG-binding domain of MBD6 from Arabidopsis thaliana.
Biomol NMR Assign 13 , 59-62 (2019)
Kunishige, R., Kano, F., *Murata, M.
The cell resealing technique for manipulating, visualizing, and elucidating molecular functions in living cells.
Biochem Biophys Acta General Subjects , In press (2019)
Kano, F., *Murata, M.
Phosphatidylinositol-3-phosphate-mediated actin domain formation linked to DNA synthesis upon insulin treatment in rat hepatoma-derived H4IIEC3 cells.
Biochem Biophys Acta Molecular Cell Research 1866 , 793-805 (2019)
Ogasawara,F., Kano, F., Murata, M. , Kimura, Y., Kioka, N., Ueda, K.
Changes in the asymmetric distribution of cholesterol in the plasma membrane influence streptolysin O pore formation.
Sci. Rep 9 , 4548 (2019)
Tanaka T, *Ikeya T, Kamoshida H, Suemoto Y, Mishima M, Shirakawa M, Güntert P, *Ito Y.
High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells.
Angew Chem Int Ed , in press (2019)
*Okamoto K, Sako Y.
Recent advances in FRET for the study of protein interactions and dynamics.
Curr Opin Struct Biol , in press (2019)
Abe S, Ito N, Maity B, Lu C, Lu D, *Ueno T.
Coordination design of cadmium ions at the 4-fold axis channel of the apo-ferritin cage.
Dalton Trans , in press (2019)
Mio M, Sugiki T, Matsuda C, Mitsuhashi H, Kojima C, Chan SY, Hayashi YK, *Mio K.
Structural instability of lamin A tail domain modulates its assembly and higher order function in Emery-Dreifuss muscular dystrophy.
Biochem Biophys Res Commun 512 , 22-28 (2019)
Lim SK, Mohamed MS, Wang H, Hartono, Hazawa M, Kobayashi A, Voon DC, Kodera N, Ando T and *Wong RW,
Direct Visualization of Avian Influenza H5N1 Hemagglutinin Precursor and its Conformational Change by High-Speed Atomic Force Microscopy.
Biochem Biophys Acta General Subjects , in press (2019)
Miyazaki R, Akiyama Y, *Mori, H,
A photo-cross-linking approach to monitor protein dynamics in living cells.
Biochem Biophys Acta General Subjects , in press (2019)
Jung J, Kobayashi C, Sugita Y,
Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step.
J. Chem. Theory Comput 15 , 84-94 (2019)
Mori T, Kulik M, Miyashita O, Jung J, Tama F, Sugita Y,
Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning.
Structure 27 , 161-174 (2019)
Miyashita O, Kobayashi C, Mori T, Sugita Y, *Tama F,
Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations,
J Comp Chem , in press (2019)
*Tsukazaki T..
Structural basis of the Sec translocon and YidC revealed through X-ray crystallography.
The Protein Journal , in press (2019)
Inoue M, Sakuta N, Watanabe A, Zhang Y, Yoshikaie K, Tanaka Y, Ushioda R, Kato Y, Takagi J, Tsukazaki T., Nagata K, and *Inaba K.
Structural Basis of Sarco/Endoplasmic Reticulum Ca2+-ATPase 2b Regulation via Transmembrane Helix Interplay.
Cell Rep 27 , 1221–1230 (2019)
Shahrizal M, Daimon Y, Tanaka Y, Hayashi Y, Nakayama S, Iwaki S, Narita S, Kamikubo H, *Akiyama Y and *Tsukazaki T.
Structural basis for the function of the β-barrel assembly-enhancing protease BepA.
J. Mol. Biol 431 , 625-635 (2019)
Haruyama T, Sugano Y, Kodera N, Uchihashi T, Ando T, Tanaka Y, *Konno H and *Tsukazaki T.
Single-unit imaging of membrane protein-embedded nanodiscs from two oriented sides by high-speed atomic force microscopy
Structure 27 , 152-160 (2019)
Hirofumi Shimizu.
Diffracted X-ray tracking method for recording single-molecule protein motions.
Biochim Biophys Acta Gen Subj , In press (2019)
Terahara N, Noguchi N, Nakamura S, Kami-ike N, Ito M, *Namba K, * Minamino T.
Load- and polysaccharide-dependent activation of the Na+-type MotPS stator in the Bacillus subtilis flagellar motor.
Sci Rep , in press (2019)
Renault TT, Abraham AO, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, *Tu Y, *Namba K, *Keener JP, *Minamino T, *Erhardt M.
Bacterial flagella grow through an injection-diffusion mechanism.
eLife , in press (2019)
Kodan A, Yamaguchi T, Nakatsu T, Matsuoka K, Kimura Y, Ueda K, Kato H.
Inward- and outward-facing X-ray crystal structures of homodimeric P-glycoprotein CmABCB1.
Nat Commun 10 , 88 (2019)
Kawanobe T, Shiranaga N, Kioka N, Kimura Y, Ueda K.
Apolipoprotein A-I directly interacts with extracellular domain 1 of human ABCA1.
Biosci Biotechnol Biochem 83 , 490-497 (2019)
Ebrahim, A., Moreno-Chicano, T., Appleby, M. V., Chaplin, A. K., Beale, J. H., Sherrell, D. A., Duyvesteyn, H. M. E., Owada, S., Tono, K., Sugimoto, H., Strange, R. W., Worrall, J. A. R., Axford, D., Owen, R. L., *Hough, M. A.
Dose-resolved serial synchrotron and XFEL structures of radiation sensitive metalloproteins.
IUCr J , in press (2019)
Sekiguchi T, Satoh T, Kurimoto E, Song C, Kozai T, Watanabe H, Ishii K, Yagi H, Yanaka S, Uchiyama S, Uchihashi T, Murata K, *Kato K.
Mutational and combinatorial control of self-assembling and disassembling of human proteasome α-subunits.
International Journal of Molecular Sciences , in press (2019)