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

2017

Papers in 2017

1.
Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy.
*Shibata M, *Nishimasu H, Kodera N, Hirano S, Ando T, Uchihashi T, *Nureki O.
Nat Commun 8 , 1430 (2017).
2.
Na+-induced structural transition of MotPS for stator assembly of the Bacillus flagellar motor.
Terahara N, Kodera N, Uchihashi T, Ando T , *Namba K, *Minamino T.
Sci Adv 3 , 4119 (2017).
3.
High-speed atomic force microscopy imaging of live mammalian cells. 
*Shibata M, Watanabe H, Uchihashi T, Ando T, Yasuda R. 
Biophys Physicobiol  14 , 127-135 (2017).
4.
High-speed XYZ nanopositioner for scanning ion conductance microscopy.
Watanabe S, * Ando T.
Appl Phys Lett 111 , 113106 (2017).
5.
Directly watching biomolecules in action by high-speed atomic force microscopy.
*Ando T.
Biophys Rev 9 , 421-429 (2017) .
6.
High-speed atomic force microscopy reveals loss of nuclear pore resilience as a dying code in colorectal cancer cells.
Mohamed MS, Kobayashi A, Taoka A, Watanabe-Nakayama T, Kikuchi Y, Hazawa M, Minamoto T, Fukumori Y, Kodera N, Uchihashi T, Ando T, *Wong RW.
ACS Nano 11 , 5567−5578 (2017).
7.
Asn-linked oligosaccharide chain of a crenarchaeon, Pyrobaculum calidifontis, is reminiscent of the eukaryotic high-mannose-type glycan.
Fujinami D, Taguchi Y, * Kohda D.
Glycobiology 27 , 701-712 (2017)
8.
Preparation of Selenoinsulin as a Long-Lasting Insulin Analogue.
Arai K, Takei T, Okumura M, Watanabe S, Amagai Y, Asahina Y, Moroder L, *Hojo H, *Inaba K, *Iwaoka M,
Angew Chem Int Ed Engl. 56(20) , 5522-5526 (2017).
9.
The Highly Dynamic Nature of ERdj5 Is Key to Efficient Elimination of Aberrant Protein Oligomers through ER-Associated Degradation.
Maegawa KI, Watanabe S, Noi K, Okumura M, Amagai Y, Inoue M, Ushioda R, Nagata K, Ogura T, *Inaba K,
Structure 25(6) , 846-857 (2017) .
10.
Structural and functional analysis of C-terminal region of FliG. An essential motor component of Vibrio Na+-driven flagella.
*Miyanoiri Y, Hijikata A, Nishino Y, Gohara M, Onoue Y, Kojima S, Kojima C, Shirai T, Kainosho M, *Homma M.
Structure 25 , 1540-1548 (2017)
11.
Stable-Isotope aided NMR Spectroscopy.
Miyanoiri Y, Takeda M, *Kainosho M.
Modern Magnetic Resonance 2 , 1-16 (2017).
12.
M. Development of an RNA aptamer that acquires binding capacity against HIV-1 Tat protein via G-quadruplex formation in response to potassium ions.
Yamaoki Y, Nagata T, Mashima T, *Katahira,
Chem commun 53 , 7056-7059 (2017).
13.
Observation by Real-Time NMR and Interpretation of Length- and Location-Dependent Deamination Activity of APOBEC3B.
Wan L, Nagata T, Morishita R, Takaori-Kondo A, *Katahira M. ACS
Chem Biol 12 , 2704-2708 (2017).
14.
Conjugation of two RNA aptamers improves binding affinity to AML1 Runt domain,
Nomura Y, Yamazaki K, Amano R, Takada K, Nagata T, Kobayashi N, Tanaka Y, Fukunaga J, Katahira M, Kozu T, Nakamura Y, Haishima Y, Torigoe H, *Sakamoto T.
J Biochem 162 , 431-436 (2017).
15.
Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA.
Iwaoka R, *Nagata T, Tsuda K, Imai T, Okano H, Kobayashi N, *Katahira M.
Molecules 22 , E1207 (2017).
16.
Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA.
Iwaoka R, *Nagata T, Tsuda K, Imai T, Okano H, Kobayashi N, *Katahira M.
Biomol NMR Assign 11 , 265-268 (2017).
17.
Crystal structure and redox properties of a novel cyanobacterial heme-protein with a His/Cys heme axial ligation and a per-arnt-sim (PAS)-like domain.
Motomura T, Suga M, Hienerwadel R, Nakagawa A, Lai T-L, Nitschke W, Kuma T, Sugiura M, Boussac A, *Shen J-R.
J Biol Chem 292 , 9959-9612 (2017).
18.
Experimental Evaluation of Density of Water in a Cell by Raman Microscopy.
Takeuchi M, Kajimoto S, *Nakabayashi T.
J Phys Chem Lett 8 , 5241-5245 (2017).
19.
Establishment and phenotyping of disease model cells created by cell-resealing technique.
Kano F, Noguchi Y, *Murata M.
Sci Rep 7 , Article number: 15167. doi:10.1038/s41598-017-15443-0 (2017).
20.
The first successful observation of in-cell NMR signals of DNA and RNA in living human cells.
Yamaoki Y, Kiyoishi A, Miyake M, Kano F, Murata M, Nagata T, Katahira M.
Phys Chem Chem Phys 20 , 2982-2985 doi:10.1039/C7CP05188C (2017).
21.
Single-molecule fluorescence imaging of RalGDS on cell surfaces during signal transduction from Ras to Ral.
Yoshizawa R, Umeki N, Yanagawa M, Murata M, Sako Y.
Biophys Physicobio 14 , 75-84. doi: 10.2142/biophysico.14.0_75 (2017).
22.
Pyruvate kinase M1 interacts with A-Raf and inhibits endoplasmic reticulum stress-induced apoptosis by activating MEK1/ERK pathway in mouse insulinoma cells.
Horiuchi Y, Nakatsu D, Kano F, *Murata M.
Cell Signal 38: , 212–222. doi: 10.1016/j.cellsig.2017.07.017(2017) .
23.
Novel prosurvival function of Yip1A in huma cervical cancer cells: constitutive activation of the IRE1 and PERK pathways of the unfolded protein response.
Taguchi Y, Horiuchi Y, Kano F, *Murata M.
Cell Death and Disease 8(3) , e2718. doi:10.1038/cddis.2017.147(2017) .
24.
High-Speed Atomic Force Microscopy Reveals Loss of Nuclear Pore Resilience as a Dying Code in Colorectal Cancer Cells.
Mohamed MS, Kobayashi A, Taoka A, Watanabe-Nakayama T, Kikuchi Y, Hazawa M, Minamoto T, Fukumori Y, Kodera N, Uchihashi T, Ando T, Wong RW*
ACS Nano 11 , 5567–5578 (2017).
25.
NMR Line Shape Analysis of a Multi-State Ligand Binding Mechanism in Chitosanase.
Shinya S, Ghinet MG, Brzezinski R, Furuita K, Kojima C, Shah S, *Kovrigin EL, *Fukamizo T.
J Biomol NMR 67 , 309-319 (2017).
26.
Cold-Shock Expression System in E. coli for Protein NMR Studies.
Sugiki T, Fujiwara T, *Kojima C.
Methods Mol Biol 1586 , 345-357 (2017).
27.
he Mechanism of the Glycosylase Reaction with hOGG1 Base-Excision Repair Enzyme: Concerted Effect of Lys249 and Asp268 During Excision of 8-Oxoguanine.
Sebera J, Hattori Y, Sato D, Reha D, Nencka R, Kohno T, *Kojima C, *Tanaka Y, *Sychrovsky V. T Nucleic
Acids Res 45 , 5231 (2017) .
28.
Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions.
Hattori Y, Heidenreich D, Ono Y, Sugiki T, Yokoyama K, Suzuki E, Fujiwara T, *Kojima C.
J Biomol NMR 68 , 271-279 (2017).
29.
Structural and functional analysis of the C-terminal region of FliG, an essential motor component of Vibrio Na+-driven flagella.
Miyanoiri Y, Hijikata A, Nishino Y, Gohara M, Onoue Y, Kojima S, Kojima C, Shirai T, Kainosho M, *Homma M.
Structure 25 , 1540-1548 (2017).
30.
Production of Single-Chain Fv Antibodies Specific for GA-Pyridine, an Advanced Glycation End-Product (AGE), with Reduced Inter-Domain Motion.
Fukuda N, Noi K, Weng L, Kobashigawa Y, Miyazaki H, Wakeyama Y, Takaki M, Nakahara Y, Tatsuno Y, Uchida-Kamekura M, Suwa Y, Sato T, Ichikawa-Tomikawa N, Nomizu M, Fujiwara Y, Ohsaka F, Saito T, Maenaka K, Kumeta H, Shinya S, Kojima C, Ogura T, *Morioka H.
Molecules 22 , 1695 (2017).
31.
BepA mediates productive transfer of substrate proteins to the β-barrel assembly machinery (BAM) complex.
Daimon Y, Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H, *Tsukazaki T, *Narita S, *Akiyama Y.
Mol Microbiol 106 , 760-776 (2017).
32.
Tunnel formation inferred from the I-form structures of the proton-driven protein secretion motor SecDF.
Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto Y V, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y, *Tsukazaki T.
Cell Reports 19 , 895-901 (2017).
33.
Impact of cellular health condition on protein folding state in mammalian cells.
Inomata K, Kamoshida H, Ikari M, Ito Y, *Kigawa T.
Chem Comm 53 , 11245-11248 (2017).
34.
Parkinson's disease-related DJ-1 functions in thiol quality control against aldehyde attack in vitro.
*Matsuda N, Kimura M, Queliconi BB, Kojima W, Mishima M, Takagi K, Koyano F, Yamano K, Mizushima T, Ito Y, *Tanaka K.
Sci Rep 7 , 12816 (2017).
35.
Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.
Kobayashi A, Kanaba T, Satoh R, Ito Y, Sugiura R, *Mishima M. Biomol.
NMR Assign 11 , 123-126 (2017).
36.
Interactions of in vitro selected fluorogenic peptide aptamers with calmodulin.
Manandhar Y, Wang W, Inoue J, Hayashi N, Uzawa T, Ito Y, Aigaki T, *Ito Y.
Biotechnol Let 39 , 375-382 (2017).
37.
Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF,
Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto Y, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y, *Tsukazaki, T.
Cell Reports 19 , 895-901 (2017).
38.
GENESIS 1.1: A Hybrid-Parallel Molecular Dynamics Simulator with Enhanced Sampling Algorithms on Multiple Computational Platforms.
Kobayashi C, Jung J, Matsunaga Y, Mori T, Ando T, Tamura K, Kamiya M, *Sugita Y.
J Comp Chem 38: , 2193-2206 (2017).
39.
Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation,
Nawrocki G, Wang P, Yu I, Sugita Y, and *Feig M,
J Phys Chem B 121 , 11072-11084 (2017).
40.
Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.
*Galvelis R, Sugita Y.
J Chem There Comp 13 , 2489-2500 (2017).
41.
Enhanced Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics,
Galvelis R, Re S, *Sugita Y.
J Chem There Comp 13 , 1934-1942 (2017).
42.
The TPR domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery complex.
Daimon Y, Iwama-Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H, * Tsukazaki T, *Narita S, *Akiyama Y.
Mol Microbiol 106 , 760-776 (2017).
43.
Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein.
Tanaka Y, Iwaki S, *Tsukazaki T.
Structure 25 , 1455-1460 (2017).
44.
SecY-SecA fusion protein retains the ability to mediate protein transport.
Sugano Y, Furukawa A, Nureki O, Tanaka Y, *Tsukazaki T.
PLOS ONE 12 , e0183434 (2017).
45.
Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF
Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto VY, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y, *Tsukazaki T.
Cell Rep 19 , 895-901 (2017).
46.
Collision with duplex DNA renders Escherichia coli DNA polymerase III holoenzyme susceptible to DNA polymerase IV-mediated polymerase switching on the sliding clamp.
Le TT, *Furukohri A, Tatsumi-Akiyama M, Maki H.
Sci Rep 7 , 12755 (2017).
47.
Parkinson's disease-related DJ-1 functions in thiol quality control against aldehyde attack in vitro.
Matsuda N, Kimura M, Queliconi BB, Kojima W, Mishima M, Takagi K, Koyano F, Yamano K, Mizushima T, Ito Y, Tanaka K.
Sci Rep 7 , 12816 (2017).
48.
Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.
Kobayashi A, Kanaba T, Satoh R, Ito Y, Sugiura R, Mishima M.
Biomol NMR Assign 11 , 123-126 (2017).
49.
Two-step process for disassembly mechanism of proteasome α7 homo-tetradecamer by α6 revealed by high-speed atomic force microscopy.
Kozai T, Sekiguchi T, Satoh T, Yagi H, *Kato K, *Uchihashi T.
Sci Rep 7 , 15373 (2017).
50.
Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acid side chains in molecular dynamics simulation.
Oroguchi, T*, Nakasako, M.
Sci Rep 7 , 15859 (2017).
51.
Controlled Terahertz Birefringence in Stretched Poly(lactic acid) Films Investigated by Terahertz Time-Domain Spectroscopy and Wide-Angle X‑ray Scattering.
Iwasaki, H, Nakamura, M, Komatsubara, N. Okano, M, Nakasako, M, Sato, H, Watanabe, S.*
J Phys Chem B 121 , 6951−6957 (2017).
52.
A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation.
Sekiguchi, Y, Hashimoto, S, Kobayashi, A, Oroguchi, T, Nakasako M. *
J Synchrotron Rad 24 , 1024–1038 (2017).
53.
An NMR approach for characterizing antibody interactions in serum environment.
Yanaka S, Yamazaki T, Yogo R, Yagi H, Kato K.
Molecules 22 , 1619 (2017).
54.
Detection of quaternary structure deformation of immunoglobulin G1 Fc glycoprotein upon interacting with a low-affinity Fc receptor by deuteration-assisted small-angle neutron scattering.
Yogo R, Yanaka S, Yagi H, Inoue R, Sato N, Sugiyama M, Kato K.
Biochem Biophys Rep 12 , 1-4 (2017) .
55.
Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa.
Sakae Y, Satoh T, Yagi H, Yanaka S, Yamaguchi T, Isoda Y, Iida S, Okamoto Y, Kato K.
Sci Rep 7 , 13780 (2017) .
56.
Elucidation of potential sites for antibody engineering by fluctuation editing.
Yanaka S, Moriwaki Y, Kouhei T, Sugase K
Sci Rep 7 , 9597 (2017).
57.
Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Tosha T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Shoji, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, *Sugimoto, H, *Shiro, Y, *Kubo, M.
Nat Commun 8 , 1585 (2017).
58.
Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Naoe, Y, Nakamura, N, Rahman, M M, Tosha, T, Nagatoishi, S, Tsumoto, K, *Shiro, Y, * Sugimoto, H.
Proteins 85 , 2217-2230 (2017).
59.
Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1.
Chase A R, Laudermilch E, Wang J, Shigematsu H, Yokoyama T, *Schlieker C.
Mol Biol Cell 28 , 2765-2772 (2017).
60.
Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain.
Hasegawa K, Someya Y, Shigematsu H, Kimura-Someya T, Nuemket N, *Kumasaka T.
Acta Crystallogr F Struct Biol Commun. 73 , 568–73 (2017).
61.
Structural basis for CRMP2-induced axonal microtubule formation.
Niwa S, Nakamura F, Tomabechi Y, Aoki M, Shigematsu H, Matsumoto T, Yamagata A, Fukai S, Hirokawa N, Goshima Y, Shirouzu M, *Nitta R.
Sci Rep 7 , 10681 (2017) .
62.
Structure of the complete elongation complex of RNA polymerase II with basal factors.
Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, *Sekine S-I.
Science 357 , 921–4 (2017) .
63.
Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G.
Iwakura N, Yokoyama T, Quaglia F, Mitsuoka K, Mio K, Shigematsu H, Shirouzu M, *Kaji A, *Kaji H.
PLoS ONE 12 , e0177972 (2017).


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