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

2016

Papers in Jan-May, 2016

1.
Comparative analysis of archaeal lipid-linked oligosaccharides that serve as oligosaccharide donors for Asn-glycosylation
Taguchi Y, Fujinami D, *Kohda D
J Biol Chem, 291 , 11042-11054 (2016).
2.
Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 mu homology domain
*Shimada A, Yamaguchi A, Kohda D
Sci Rep 6 , 19565 (2016).
3.
Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules
Matsuoka R, Shimada A, Komuro Y, Sugita Y, *Kohda D
Protein Sci 25 , 754-768 (2016).
4.
Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Yokogawa M, Tsushima T, Noda NN, Kumeta H, Enokizono Y, Yamashita K, Standley DM, Takeuchi O, Akira S, *Inagaki F
Sci Rep 6 , 22324 (2016).
5.
Nuclear magnetic resonance analysis of the conformational state of cancer mutant of fibroblast growth factor receptor 1 tyrosine kinase domain
Kobashigawa Y, Amano S, Yoza K, Himeno R, Amemiya S, Morioka H, Yokogawa M, Kumeta H, Schlessinger J, *Inagaki F
Genes Cells 21 , 350-357 (2016).
6.
Functional extension of high-speed atomic force microscopy
Uchihashi T, Watanabe H, Fukuda S, Shibata M, *Ando T
Ultramicroscopy 160 , 182-196 (2016).
7.
Where the complex things are: single molecule andensemble spectroscopic investigations of protein folding dynamics
*Takahashi S, Kamagata K, Oikawa H
Curr Opin Struct Biol 36 , 1-9 (2016).
8.
Cysteines 208 and 241 in Ero1α are required for maximal catalytic turnover
Ramming T, Kanemura S, Okumura M, *Inaba K, *Appenzeller-Herzog C
Redox Biology 7 , 14-20 (2016).
9.
Augmin shapes the anaphase spindle for efficient cytokinetic furrow ingression and abscission
*Uehara R, Kamasaki T, Hiruma S, Poser I, Yoda K, Yajima J, Gerlich DW, Goshima G
Molecular Biology of the Cell 27 , 812-827 (2016).
10.
Characterization of the deamination coupled with sliding along DNA of anti-HIV factor APOBEC3G on the basis of the pH-dependence of deamination revealed by real-time NMR monitoring
Kamba K, *Nagata T, *Katahira M
Front Microbiol 7 ,587 (2016).
  
11.
Effect of the N-terminal residues on the quaternary dynamics of human adult hemoglobin
Chang S, Mizuno M, Ishikawa H, *Mizutani Y
Chem. Phys. 469-470 , 31-37 (2016).
12.
Chromophore structure of photochromic fluorescent protein dronpa: acid-base equilibrium of two cis configurations
Higashino A, Mizuno M, *Mizutani Y
J. Phys. Chem. B. 120 , 3353-3359 (2016).
13.
Structure and energy transfer pathways of the plant photosystem I-LHCI supercomplex
Suga M, Qin X, *Kuang T, *Shen JR
Curr Opin in Struct Biol, 39 , 46-53 (2016).
14.
Filopodia Formation by Cross-linking of F-actin with Fascin in Two Different Binding Manners
Aramaki S, Mayanagi K, Jin, M, Aoyama, K, *Yasunaga T
Cytoskeleton 73, 365-374 (2016).
 
15.
Structural insight into photoactivation of an adenylate cyclase from a photosynthetic cyanobacterium
Ohki M, Sugiyama K, Kawai F, Tanaka H, Nihei Y, Unzai S, Takebe M, Matsunaga S, Adachi S, Shibayama N, Zhou Z, Koyama R, Ikegaya Y, Takahashi T, Tame J, Iseki M, Park S-Y
Proc Natl Acad Sci USA 113, 6659-6664 (2016).
16.
An intrinsically disordered protein Atg13 mediates supramolecular assembly of autophagy initiation complexes
Yamamoto H, Fujioka Y, Suzuki SW, Noshiro D, Suzuki H, Kondo-Kakuta C, Kimura Y, Hirano H, Ando T, *Noda NN, *Ohsumi Y
Dev Cell 38, 86-99 (2016).
17.
F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements
*Sugawa M, Okazaki K, Kobayashi M, Matsui T, Hammer G, Masaike T, *Nishizaka T
Proc. Natl. Acad. Sci. U.S.A. 113, E2916-2924 (2016).
18.
Efficient identification and analysis of chemical exchange in biomolecules by R1ρ relaxation dispersion with Amaterasu
Walinda E, Morimoto D, Nishizawa M, Shirakawa M, *Sugase K
Bioinformatics 32, 2539-2541 (2016).
19.
Moderate plasma treatment enhances the quality of optically detected magnetic resonance signals of nitrogen-vacancy centres in nanodiamonds
Sotoma S, *Igarashi R, *Shirakawa M
Applied Physics A 122 , 522 (2016).
20.
Selective labeling of proteins on living cell membranes using fluorescent nanodiamond probes
Sotoma S,Iimura J, Igarashi R , Hirosawa KM , Ohnishi H, Mizukami S, Kikuchi K, Fujiwara TK, *Shirakawa M, *Tochio, H
Nanomaterials 6 , 56 (2016).
21.
Arrayed water-in-oil droplet bilayers for membrane transport analysis
*Watanabe R, Soga N, Hara M, Noji H
Lab Chip 16, 3043-3048 (2016).
22.
Novel Nano-Device to Measure Voltage-Driven Membrane Transporter Activity
*Watanabe R, Soga N, Noji H
Trans Nanotech 15 , 70-73 (2016).
23.
Selective Labeling of Proteins on Living Cell Membranes Using Fluorescent Nanodiamond Probes
Sotoma S, Iimura J, Igarashi R, Hirosawa KM, Ohnishi H, Mizukami S, Kikuchi K, Fujiwara KT, *Shirakawa M, *Tochio H
Nanomaterials 6 , 56-64 (2016).
24.
Allosteric activation of glutamate receptors by on-cell coordination chemistry
*Kiyonaka S, Kubota R, Michibata Y, Sakakura M, Takahashi H, Numata T, Inoue R, Yuzaki M, *Hamachi I
Nat Chem 8, 958-967 (2016)
25.
Protein NMR Structure Refinement based on Bayesian Inference
*Ikeya T, Ikeda S, Kigawa T, Ito Y, Güntert P
J Phys: Conf Ser 699 , 1-14 (2016).
26.
Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
Takaharu Mori, Naoyuki Miyashita, Wonpil Im, Michael Feig, *Yuji Sugita
BBA-biomembranes 1858, 1635-1651 (2016) .
27.
Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules
Rei Matsuoka, Atsushi Shimada, Yasuaki Komuro, Yuji Sugita, *Daisuke Kohda
Protein Sci. 25 , 754-768 (2016).
28.
Rearrangements of α-helical structures of FlgN chaperone control the binding affinity for its cognate substrates during flagellar type III export
Kinoshita M, Nakanishi Y, Furukawa Y, Namba K, *Imada K, *Minamino T
Mol. Microbiol. 101, 656-670 (2016).
29.
Insight into the flagellar type III protein export revealed by the complex structure of the type III ATPase and its regulator
*Imada K, Minamino T, Uchida Y, Kinoshita M, Namba K
Proc. Natl. Acad. Sci. USA 113 , 3633–3638 (2016).
30.
The bacterial flagellar type III export gate complex is a dual fuel engine that can use both H+ and Na+ for flagellar protein export
*Minamino T, Morimoto YV, Hara N, Aldridge PD, *Namba K
PLoS Pathog. 12 , e1005495 (2016)
31.
FliH and FliI ensure efficient energy coupling of flagellar type III protein export in Salmonella
*Minamino T, Kinoshita M, Inoue Y, Morimoto YV, Ihara K, Koya S, Hara N, Nishioka N, Kojima S, Homma M, *Namba K
MicrobiologyOpen 5, 424-435 (2016) .
32.
Higher-order assemblies of BAR domain proteins for shaping membranes
*Suetsugu S
Microscopy 65, 201-210 (2016) .
33.
Yeast Ivy1p Is a Putative I-BAR-domain Protein with pH-sensitive Filament Forming Ability in vitro
Itoh Y, Kida K, Hanawa-Suetsugu K, Suetsugu S
Cell Struct Funct. 41 , 1-11 (2016).
34.
Changes in hydration structure regulate collective motions of a multi-domain protein
Oroguchi T, *Nakasako M
Sci Rep 6, 26302 (2016).
35.
Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate statistics
Sekiguchi Y, Oroguchi T, *Nakasako M
J. Synchrotron Rad. 23 , 312-323 (2016).
36.
Quantitative analysis of protein–ligand interactions by NMR
Furukawa A, Konuma T, Yanaka S, Sugase K
Progress in Nuclear Magnetic Resonance Spectroscopy 96 , 47-57 (2016).
37.
A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline
Sakaguchi M, Kimura T, Nishida T, Tosha T, Sugimoto H, Yamaguchi Y, Yanagisawa S, Ueno G, Murakami H, Ago H, Yamamoto M, Ogura T, Shiro Y, *Kubo M
J. Synchrotron Rad 23 , 334-338 (2016).
38.
Structure of a group II intron in complex with its reverse transcriptase
Qu G, Kaushal P S, Wang J, Shigematsu H, Piazza C L, *Agrawal R K, *Marlene B, *Wang H-W
Nat Struc & Mol Biol 23, 549-557 (2016).
39.
Self-assembly of size-controlled liposomes on DNA nanotemplates
Yang Y, Wang J, Shigematsu H, Xu W, *Shih W M, *Rothman J E, *Lin C
Nature Chemistry 8 , 476–483 (2016).
40.
Statistical modeling and removal of lipid membrane projections for cryo-EM structure determination of reconstituted membrane proteins
*Jensen KH, Brandt SS, Shigematsu H, Sigworth F J
Journal of Structural Biology 194 , 49–60 (2016).
41.
Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC
Jeong H, Kim J-S, Song S, Shigematsu H, Yokoyama T, *Hyun J, *Ha N-C
Structure 24 , 272–276 (2016).

Papers in Jun-Dec, 2016

42.
Trisaccharide containing α2,3-linked sialic acid is a receptor for mumps virus
Kubota M, *Takeuchi K, Watanabe S, Ohno S, Matsuoka R, Kohda D, Nakakita SI, Hiramatsu H, Suzuki Y, Nakayama T, Terada T, Shimizu K, Shimizu N, Shiroishi M, Yanagi Y, *Hashiguchi T.
Proc Natl Acad Sci U S A 113 , 11579-11584 (2016).
43.
Chaperonin GroEL-GroES functions as both alternating and non-alternating engines
Yamamoto D, *Ando T.
J Mol Biol 428 , 3090-3101 (2016).
44.
The intrinsically disordered protein Atg13 mediates supramolecular assembly of autophagy initiation complexes
Yamamoto H, Fujioka Y, Suzuki SW, Noshiro D, Suzuki H, Kondo-Kakuta C, Kimura Y, Hirano H, Ando T, *Noda, NN, Ohsumi Y.
Dev Cell 38 , 86–99 (2016).
45.
High-speed atomic force microscopy reveals strongly polarized movement of clostridial collagenase along collagen fibrils
Watanabe-Nakayama T, Itami M, Kodera N, Ando T, *Konno H.
Sci Rep 6 , 28975 (2016).
46.
NMR Structural Biology Using Paramagnetic Lanthanide Probe
Saio T, *Inagaki F.
In Advanced Methods in Structural Biology (pp. 315–340). Tokyo: Springer Japan , (2016).
47.
Activation of p53 facilitates the target search in DNA by enhancing the target recognition probability
Itoh Y., Murata A., Sakamoto S., Nanatani K., Wada T., *Takahashi S. and *Kamagata K.
J. Mol. Biol. 428 , 2916-2930 (2016).
48.
Human Ero1α undergoes dual regulation through complementary redox interactions with PDI
Kanemura S, Okumura M, K. Yutani, Ramming T, Hikima T, Appenzeller-Herzog C, Akiyama S, *Inaba K.
J. Biol. Chem. 291 , 23952-23964 (2016) .
49.
Redox-assisted regulation of Ca2+ homeostasis in the endoplasmic reticulum by ERdj5
Ushioda R, Miyamoto A, Inoue M, Watanabe S, Okumura M, Maegawa K, Uegaki K, Fujii S, Fukuda Y, Umitsu M, Takagi J, Inaba K, Mikoshiba K, *Nagata K.
Proc Natl Acad Sci USA 113 , E6055-6063 (2016).
50.
Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility
Yamagishi M, Shigematsu H, Yokoyama T, Kikkawa M, Sugawa M, Aoki M, Shirouzu M, *Yajima J, and *Nitta R.
Structure 24 , 1322-1334 (2016).
 
51.
Accurate and molecular-size-tolerant NMR quantitation of diverse components in solution
Okamura H, Nishimura H, Nagata T, Kigawa T, Watanabe T, *Katahira M.
Sci Rep 6 , 21742 (2016).
52.
Structure, Dynamics, and Interaction of p54(nrb)/NonO RRM1 with 5' Splice Site RNA Sequence
Duvignaud JB, Bédard M, Nagata T, Muto Y, Yokoyama S, Gagné SM, *Vincent M.
Biochemistry 55 , 2553-2566 (2016).
53.
The binding specificity of translocated in liposarcoma/fused in sarcoma with lncRNA transcribed from the promoter region of cyclin D1
Yoneda R, Suzuki S, Mashima T, Kondo K, Nagata T, Katahira M, *Kurokawa R.
Cell Biosci 6 , 4 (2016).
54.
A Study of the Dynamics of the Heme Pocket and C-helix in CooA Upon CO Dissociation Using Time-resolved Visible and UV Resonance Raman Spectroscopy
Otomo A, Ishikawa H, Mizuno M, Kimura T, Kubo M, Shiro Y, Aono S, *Mizutani Y.
J. Phys. Chem. B 120 , 7836-7843 (2016).
55.
Regulatory Implications of Structural Changes in Tyr201 of the Oxygen Sensor Protein FixL
Yamawaki T, Ishikawa H, Mizuno M, Nakamura H, Shiro Y, *Mizutani Y.
Biochemistry 55 , 4027-4035 (2016).
56.
Importance of Atomic Contacts in Vibrational Energy Flow in Proteins
Kondoh M, Mizuno M, *Mizutani Y.
J. Phys. Chem. Lett. 7 , 1950-1954 (2016).
57.
Development of an X-ray fluorescence holographic measurement system for protein crystals
*Sato-Tomita A, *Shibayama N, Happo N, Kimura K, Okabe T, Matsushita T, Park S-Y, Sasaki Y, *Hayashi K.
Review of Scientific Instruments 87 , 063707 (2016).
58.
A simple method for ion channel recordings using fine gold electrode
Okuno, D., Hirano, M., Yokota, H. , Onishi, Y., Ichinose, J., *Ide, T.
Anal. Sci. 32 , 1353-1357 (2016).
59.
Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility
Yamagishi M, Shigematsu H, Yokoyama T, Kikkawa M, Sugawa M, Aoki M, Shirouzu M, *Yajima J, *Nitta R.
Structure 24 , 1322-1334 (2016).
60.
Ubiquitylation Directly Induces Fold Destabilization of Proteins
Morimoto D, Walinda E, Fukada H, Sugase K, *Shirakawa M.
Sci Rep 19 , 39453 (2016).
61.
A Nanodiamond-peptide Bioconjugate for Fluorescence and ODMR Microscopy of a Single Actin Filament
Genjo T, Sotoma S, Tanabe R, *Igarashi R, Shirakawa M.
Anal Sci 32 , 1165-1170 (2016).
62.
Dual Function of Phosphoubiquitin in E3 Activation of Parkin
Walinda E, Morimoto D, Sugase K , *Masahiro Shirakawa.
J Biol Chem 291 , 16879-16879 (2016).
63.
The evolving world of ubiquitin: transformed polyubiquitin chains
*Morimoto D, Shirakawa M.
Biomol Concepts 7 , 157-167 (2016).
64.
Monodispersed Colloidal Solutions of Surface-modified Detonation-synthesized Nanodiamonds and Their Aggregation Resistance
Sotoma S, *Shirakawa M.
Chem Lett 45 , 697-699 (2016).
65.
Utilization of paramagnetic relaxation enhancements for structural analysis of actin-binding proteins in complex with actin
Huang S, Umemoto R, Tamura Y, Kofuku Y, Uyeda TQP, Nishida N, *Shimada I.
Sci Rep 6 , 33690 (2016).
66.
13C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI)
Takeda M, Miyanoiri Y, Terauchi T, *Kainosho M.
J Biomol NMR 66 , 37-53 (2016).
67.
Highly efficient residue-selective labeling with isotope-labeled Ile, Leu, and Val using a new auxotrophic E. coli strain
Miyanoiri Y, Ishida Y, Takeda M, Terauchi T, Inouye M, *Kainosho M.
J Biomol NMR 65 , 109-119 (2016).
68.
Selective Labeling of Proteins on Living Cell Membranes Using Fluorescent Nanodiamond Probes
Sotoma S, Iimura J, Igarashi R, Hirosawa KM, Ohnishi H, Mizukami S, Kikuchi K, Fujiwara KT, *Shirakawa M, *Tochio H.
Nanomaterials 6 , 56-64 (2016).
69.
Discovery of allosteric modulators for GABAa receptors by ligand-directed chemistry
Yamaura K, *Kiyonaka S, Numata T, Inoue R, *Hamachi I.
Nat Chem. Biol. 12 , 822-830 (2016).
70.
State transition analysis of spontaneous branch migration of the Holliday junction by photon-based single-molecule fluorescence resonance energy transfer
Okamoto K, *Sako Y.
Biophys. Chem. 209 , 21–27 (2016).
71.
Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M
eLife 5 , e19274 (2016).
72.
Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations
Jung J, Naruse A, Kobayashi C, Sugita Y
J. Chem. Theory Comput. 12 , 4947-4958 (2016).
73.
Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations
Otaki H, Yagi K, Ishiuchi S, Fujii M, Sugita Y
J. Phys. Chem. B 120 , 10199-10213 (2016).
74.
Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter
Nishima W, Mizukami W, Tanaka Y, Ishitani R, Nureki O, *Sugita Y
Biophys. J. 110 , 1346-1354 (2016).
75.
Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory
Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano S, and *Sugimoto N
Chem. Phys. Lett. 660 , 250-255 (2016).
76.
Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns
Tokuhisa A, Jonic S, Tama F, *Miyashita O.
J Struct Biol. 194 , 325-336 (2016).
77.
High-resolution pH imaging of living bacterial cell to detect local pH differences
Morimoto YV, Kami-ike N, Miyata T, Kawamoto A, Kato T, *Namba K, * Minamino T.
mBio 7 , 1911-1916 (2016).
78.
Structural stability of flagellin subunit affects the rate of flagellin export in the absence of FliS chaperone
Furukawa Y, Inoue Y, Sakaguchi A, Mori Y, Miyata T, *Namba K, *Minamino T.
Mol. Microbiol. 102 , 405–416 (2016).
79.
Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging
Kameda H, Usugi S, Kobayashi M, Fukui N, Lee S, Hongo K, Mizobata T, Sekiguchi Y, Masaki Y, Kobayashi A, Oroguchi T, Nakasako M, Takayama Y, Yamamoto M, *Kawata Y.
J Biochem. (Tokyo) 161 , 55-65 (2016).
80.
Blue-light-excited LOV2 triggers a rearrangement of the kinase domain to induce phosphorylation activity in Arabidopsis phototropin
Oide M, *Okajima K, Kashojiya S, Takayama Y, Oroguchi T, Hikima T, Yamamoto M, Nakasako M.
J Biol Chem 291 , 19975–19984 (2016).
81.
Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and organelles using X-ray free electron laser at SACLA
Kobayashi A, Sekiguchi Y, Oroguchi T, Okajima K, Fukuda A, Oide M, Yamamoto M, *Nakasako M.
J Synchrotron Rad 23 , 975–989 (2016).
82.
Crystal structure of bacterial heme importer complex in the inward-facing conformation
Naoe Y, Nakamura N, Doi A, Sawabe M, Nakamura H, Shiro Y, *Sugimoto H.
Nat. Commun. 7 , 134111 (2016).



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