研究代表者を二重下線で研究分担者を下線で示してあります。
2023
稲葉班・水上班の共同研究
Amagai Y, Yamada M, Kowada T, Watanabe T, Du Y, Liu R, Naramoto S, Watanabe S, Kyozuka J, Anelli T, Tempio T, Sitia R, Mizukami S, Inaba K
Zinc homeostasis governed by Golgi-resident ZnT family members regulates ERp44-mediated proteostasis at the ER-Golgi interface
Nat. Commun. (2023) DOI: 10.1038/s41467-023-38397-6
稲葉班・吉川班の共同研究
Chen Z, Watanabe S, Hashida H, Inoue M, Daigaku Y, Kikkawa M, Inaba K
Cryo-EM structures of human SPCA1a reveal the mechanism of Ca2+/Mn2+ transport into the Golgi apparatus
Science Advances (2023) DOI: 10.1126/sciadv.add9742
Hiyamizu S, Qiu H, Vuolo L, Stevenson NL, Shak C, Heesom KJ, Hamada Y, Tsurumi Y, Chiba S, Katoh Y, Stephens DJ, Nakayama K
Multiple interactions of the dynein-2 complex with the IFT-B complex are required for effective IFT
J. Cell Sci. (2023) DOI: 10.1242/jcs.260462
Niitsu A, Sugita Y
Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation
Phys. Chem. Chem. Phys. (2023) DOI: 10.1039/d2cp03972a
水上班・杉田班の共同研究
Sarkar HS, Mashita T, Kowada T, Hamaguchi S, Sato T, Kasahara K, Matubayasi N, Matsui T, Mizukami S
Arylazopyrazole-based photoswitchable inhibitors selective for Escherichia coli dihydrofolate reductase
ACS Chem. Biol. (2023) DOI: 10.1021/acschembio.2c00749
Eisenstein F, Yanagisawa H, Kashihara H, Kikkawa M, Tsukita S, Danev R
Parallel cryo electron tomography on in situ lamellae
Nat. Methods (2023) DOI: 10.1038/s41592-022-01690-1
Toyooka K, Goto Y, Hashimoto K, Wakazaki M, Sato M, Hirai MY
Endoplasmic reticulum bodies in the lateral root cap are involved in the direct transport of beta-glucosidase to vacuoles
Plant Cell Physiol. (2023) DOI: 10.1093/pcp/pcac177
Yamamoto H, Zhang S, Mizushima N
Autophagy genes in biology and disease
Nat. Rev. Genet. (2023) DOI: 10.1038/s41576-022-00562-w
Lim K, Nishide G, Sajidah ES, Yamano T, Qiu Y, Yoshida T, Kobayashi A, Hazawa M, Ando T, Hanayama R, Wong RW
Nanoscopic assessment of anti-SARS-CoV-2 spike neutralizing antibody using high-speed AFM
Nano Lett. (2023) DOI: 10.1021/acs.nanolett.2c04270
Chiba K, Kita T, Anazawa Y, Niwa S
Insight into the regulation of axonal transport from the study of KIF1A-associated neurological disorder
J. Cell Sci. (2023) DOI: 10.1242/jcs.260742
2022
稲葉班・杉田班・吉川班の共同研究
Zhang Y, Kobayashi C, Cai X, Watanabe S, Tsutsumi A, Kikkawa M, Sugita Y, Inaba K
Multiple sub-state structures of SERCA2b reveal conformational overlap at transition steps during the catalytic cycle
Cell Rep. (2022) DOI: 10.1016/j.celrep.2022.111760
Okita K, Kasahara K, Matubayasi N
Diffusion theory of molecular liquids in the energy representation and application to solvation dynamics
J. Chem. Phys. (2022) DOI: 10.1063/5.0125432
Matsunaga Y, Kamiya M, Oshima H, Jung J, Ito S, Sugita Y
Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation
Biophys. Rev. (2022) DOI: 10.1007/s12551-022-01030-9
Taoka K-I, Kawahara I, Shinya S, Harada K-I, Yamashita E, Shimatani Z, Furuita K, Muranaka T, Oyama T, Terada R, Nakagawa A, Fujiwara T, Tsuji H, Kojima C
Multifunctional chemical inhibitors of the florigen activation complex discovered by structure-based high-throughput screening
Plant J. (2022) DOI: 10.1111/tpj.16008
Murakoshi H, Ueda HH, Goto R, Hamada K, Nagasawa Y, Fuji T
In vivo three- and four-photon fluorescence microscopy using a 1.8 µm femtosecond fiber laser system
Biomed. Opt. Express (2022) DOI: 10.1364/BOE.477322
Dokainish HM, Sugita Y
Structural effects of spike protein D614G mutation in SARS-CoV-2
Biophys. J. (2022) DOI: 10.1016/j.bpj.2022.11.025
Mori A, Masuda T, Ito S, Ohtsuki S
Human hepatic transporter signature peptides for quantitative targeted absolute proteomics: selection, digestion efficiency, and peptide stability
Pharm. Res. (2022) DOI: 10.1007/s11095-022-03387-8
Sajidah ES, Lim K, Yamano T, Nishide G, Qiu Y, Yoshida T, Wang H, Kobayashi A, Hazawa M, Dewi FRP, Hanayama R, Ando T, Wong RW
Spatiotemporal tracking of small extracellular vesicle nanotopology in response to physicochemical stresses revealed by HS-AFM
J. Extracell. Vesicles (2022) DOI: 10.1002/jev2.12275
Hayakawa Y, Takaine M, Ngo KX, Imai T, Yamada MD, Behjat AB, Umeda K, Hirose K, Yurtsever A, Kodera N, Tokuraku K, Numata O, Fukuma T, Ando T, Nakano K, Uyeda TQ
Actin-binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II
Life Sci. Alliance (2022) DOI: 10.26508/lsa.202201469
Yurtsever A, Wang P-X, Priante F, Morais Jaques Y, Miyazawa K, MacLachlan MJ, Foster AS, Fukuma T
Molecular insights on the crystalline cellulose-water interfaces via three-dimensional atomic force microscopy
Sci. Adv. (2022) DOI: 10.1126/sciadv.abq0160
Yamamoto T, Yasuda S, Kasai RS, Nakano R, Hikiri S, Sugaya K, Hayashi T, Ogasawara S, Shiroishi M, Fujiwara T, Kinoshita M, Murata T
A methodology for creating mutants of G-protein coupled receptors stabilized in active state by combining statistical thermodynamics and evolutionary molecular engineering
Protein Sci. (2022) DOI: 10.1002/pro.4425
Ohshima T, Yamamoto H, Sakamaki Y, Saito C, Mizushima N
NCOA4 drives ferritin phase separation to facilitate macroferritinophagy and microferritinophagy
J. Cell Biol. (2022) DOI: 10.1083/jcb.202203102
Furuita K, Inomata K, Sugiki T, Kobayashi N, Fujiwara T, Kojima C
1H, 13C, and 15N resonance assignments of human glutathione peroxidase 4
Biomol. NMR Assign. (2022) DOI: 10.1007/s12104-022-10090-7
Matsubara D, Kasahara K, Dokainish HM, Oshima H, Sugita Y
Modified protein-water interactions in CHARMM36m for thermodynamics and kinetics of proteins in dilute and crowded solutions
Molecules (2022) DOI: 10.3390/molecules27175726
Yurtsever A, Wang P-X, Priante F, Morais Jaques Y, Miyata K, MacLachlan MJ, Foster AS, Fukuma T
Probing the structural details of chitin nanocrystal-water interfaces by three-dimensional atomic force microscopy
Small Methods (2022) DOI: 10.1002/smtd.202200320
Yamada H, Abe T, Nagaoka H, Takashima E, Nitta R, Yamamoto M, Takei K
Recruitment of Irgb6 to the membrane is a direct trigger for membrane deformation
Front. Cell. Infect. Microbiol. (2022) DOI: 10.3389/fcimb.2022.992198
仁田班・丹羽班の共同研究
Taguchi S, Nakano J, Imasaki T, Kita T, Saijo-Hamano Y, Sakai N, Shigematsu H, Okuma H, Shimizu T, Nitta E, Kikkawa A, Mizobuchi S, Niwa S, Nitta R
Structural model of microtubule dynamics inhibition by kinesin-4 from the crystal structure of KLP-12 -tubulin complex
eLife (2022) DOI: 10.7554/eLife.77877
Masuda-Ozawa T, Fujita S, Nakamura R, Watanabe H, Kuranaga E, Nakajima Y-I
siRNA-mediated gene knockdown via electroporation in hydrozoan jellyfish embryos
Sci. Rep. (2022) DOI: 10.1038/s41598-022-20476-1
Yim WW-Y, Yamamoto H, Mizushima N
A HaloTag-based reporter processing assay to monitor autophagic flux
Autophagy (2022) DOI: 10.1080/15548627.2022.2123638
Oide M, Sugita Y
Protein folding intermediates on the dimensionality reduced landscape with UMAP and native contact likelihood
J. Chem. Phys. (2022) DOI: 10.1063/5.0099094
Yim WW-Y, Yamamoto H, Mizushima N
A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag
eLife (2022) DOI: 10.7554/eLife.78923
Tanaka S, Yamamoto N, Kasahara K, Ishii Y, Matubayasi N
Crystal growth of urea and its modulation by additives as analyzed by all-atom MD simulation and solution theory
J. Phys. Chem. B (2022) DOI: 10.1021/acs.jpcb.2c01764
Nakatani K, Teshigawara S, Tanahashi Y, Kasahara K, Higashi M, Sato H
Solvation in nitration of benzene and the valence electronic structure of the Wheland intermediate
Phys. Chem. Chem. Phys. (2022) DOI: 10.1039/d2cp01699k
Ngo KX, Nguyen PDN, Furusho H, Miyata M, Shimonaka T, Chau NNB, Vinh NP, Nghia NA, Mohammed TO, Ichikawa T, Kodera N, Konno H, Fukuma T, Quoc NB
Unraveling the host-selective toxic interaction of cassiicolin with lipid membranes and its cytotoxicity
Phytopathology (2022) DOI: 10.1094/PHYTO-09-21-0397-R
Hirano M, Ando R, Shimozono S, Sugiyama M, Takeda N, Kurokawa H, Deguchi R, Endo K, Haga K, Takai-Todaka R, Inaura S, Matsumura Y, Hama H, Okada Y, Fujiwara T, Morimoto T, Katayama K, Miyawaki A
A highly photostable and bright green fluorescent protein
Nat. Biotechnol. (2022) DOI: 10.1038/s41587-022-01278-2
Shinya S, Katahira R, Furuita K, Sugiki T, Lee Y-H, Hattori Y, Takeshita K, Nakagawa A, Kokago A, Akagi K-I, Oouchi M, Hayashi F, Kigawa T, Takimoto-Kamimura M, Fujiwara T, Kojima C
19F chemical library and 19F-NMR for a weakly bound complex structure
RSC Med. Chem. (2022) DOI: 10.1039/d2md00170e
Harada K-I, Furuita K, Yamashita E, Taoka K-I, Tsuji H, Fujiwara T, Nakagawa A, Kojima C
Crystal structure of potato 14-3-3 protein St14f revealed the importance of helix I in StFDL1 recognition
Sci. Rep. (2022) DOI: 10.1038/s41598-022-15505-y
Sumikama T, Federici Canova F, Gao DZ, Penedo M, Miyazawa K, Foster AS, Fukuma T
Computed three-dimensional atomic force microscopy images of biopolymers using the Jarzynski equality
J. Phys. Chem. Lett. (2022) DOI: 10.1021/acs.jpclett.2c01093
Uechi H, Fukushima K, Shirasawa R, Sekine S, Kuranaga E
Inhibition of negative feedback for persistent epithelial cell-cell junction contraction by p21-activated kinase 3
Nat. Commun. (2022) DOI: 10.1038/s41467-022-31252-0
Oda T, Yanagisawa H, Shinmori H, Ogawa Y, Kawamura T
Cryo-electron tomography of Birbeck granules reveals the molecular mechanism of langerin lattice formation
eLife (2022) DOI: 10.7554/eLife.79990
Ito S, Yagi K, Sugita Y
Computational analysis on the allostery of tryptophan synthase: relationship between α/β-ligand binding and distal domain closure
J. Phys. Chem. B (2022) DOI: 10.1021/acs.jpcb.2c01556
Ichikawa T, Wang D, Miyazawa K, Miyata K, Oshima M, Fukuma T
Chemical fixation creates nanoscale clusters on the cell surface by aggregating membrane proteins
Commun. Biol. (2022) DOI: 10.1038/s42003-022-03437-2
Novianti I, Kowada T, Mizukami S
Clip to Click: controlling inverse electron-demand Diels-Alder reactions with macrocyclic tetrazines
Org. Lett. (2022) DOI: 10.1021/acs.orglett.2c01010
Shinobu A, Re S, Sugita Y
Practical protocols for efficient sampling of kinase-inhibitor binding pathways using two-dimensional replica-exchange molecular dynamics
Front. Mol. Biosci. (2022) DOI: 10.3389/fmolb.2022.878830
Heo L, Sugita Y, Feig M
Protein assembly and crowding simulations
Curr. Opin. Struct. Biol. (2022) DOI: 10.1016/j.sbi.2022.102340
Tan C, Jung J, Kobayashi C, Torre DUL, Takada S, Sugita Y
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
PLoS Comput. Biol. (2022) DOI: 10.1371/journal.pcbi.1009578
Dokainish HM, Re S, Mori T, Kobayashi C, Jung J, Sugita Y
The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein
eLife (2022) DOI: 10.7554/eLife.75720
水上班・稲葉班の共同研究
Liu R, Kowada T, Du Y, Amagai Y, Matsui T, Inaba K, Mizukami S
Organelle-level labile Zn2+ mapping based on targetable fluorescent sensors
ACS Sens. (2022) DOI: 10.1021/acssensors.1c02153
Nakagawa Y, Shen HC-H, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, Taguchi H, Tanaka M
Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system
Nat. Chem. Biol. (2022) DOI: 10.1038/s41589-021-00951-y
Kikkawa M, Yanagisawa H
Identifying proteins in the cell by tagging techniques for cryo-electron microscopy
Microscopy (2022) DOI: 10.1093/jmicro/dfab059
Hui KK, Endo R, Sawa A, Tanaka M
A perspective on the potential involvement of impaired proteostasis in neuropsychiatric disorders
Biol. Psychiatry (2022) DOI: 10.1016/j.biopsych.2021.09.001
Higashida M, Niwa S
Dynein intermediate chains DYCI-1 and WDR-60 have specific functions in Caenorhabditis elegans
Genes Cells (2022) DOI: 10.1111/gtc.12996
仁田班・丹羽班の共同研究
Imasaki T, Kikkawa S, Niwa S, Saijo-Hamano Y, Shigematsu H, Aoyama K, Mitsuoka K, Shimizu T, Aoki M, Sakamoto A, Tomabechi Y, Sakai N, Shirouzu M, Taguchi S, Yamagishi Y, Setsu T, Sakihama Y, Nitta E, Takeichi M, Nitta R
CAMSAP2 organizes a γ-tubulin-independent microtubule nucleation centre through phase separation
eLife (2022) DOI: 10.7554/eLife.77365
2021
Penedo M, Miyazawa K, Okano N, Furusho H, Ichikawa T, Alam MS, Miyata K, Nakamura C, Fukuma T
Visualizing intracellular nanostructures of living cells by nanoendoscopy-AFM
Sci. Adv. (2021) DOI: 10.1126/sciadv.abj4990
Barabás K, Kobolák J, Godó S, Kovács T, Ernszt D, Kecskés M, Varga C, Jánosi TZ, Fujiwara T, Kusumi A, Téglási A, Dinnyés A, Ábrahám IM
Live-cell imaging of single Neurotrophin receptor molecules on human neurons in Alzheimer’s disease
Int. J. Mol. Sci. (2021) DOI: 10.3390/ijms222413260
Danev R, Yanagisawa H, Kikkawa M
Cryo-EM performance testing of hardware and data acquisition strategies
Microscopy (2021) DOI: 10.1093/jmicro/dfab016
Kasahara K, Masayama R, Okita K, Matubayasi N
Atomistic description of molecular binding processes based on returning probability theory
J. Chem. Phys. (2021) DOI: 10.1063/5.0070308
Puppulin L, Kanayama D, Terasaka N, Sakai K, Kodera N, Umeda K, Sumino A, Marchesi A, Weilin W, Tanaka H, Fukuma T, Suga H, Matsumoto K, Shibata M
Macrocyclic peptide-conjugated tip for fast and selective molecular recognition imaging by high-speed atomic force microscopy
ACS Appl. Mater. Interfaces (2021) DOI: 10.1021/acsami.1c17708
Yurtsever A, Das S, Nishimura T, Rodríguez R, Hirose D, Miyata K, Sumino A, Fukuma T, Maeda K
Visualisation of helical structures of poly(diphenylacetylene)s bearing chiral amide pendants by atomic force microscopy
Chem. Commun. (2021) DOI: 10.1039/d1cc05341h
Saijo-Hamano Y, Sherif AA, Pradipta A, Sasai M, Sakai N, Sakihama Y, Yamamoto M, Standley DM, Nitta R
Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6
Life Sci. Alliance (2021) DOI: 10.26508/lsa.202101149
稲葉班・吉川班の共同研究
Zhang Y, Watanabe S, Tsutsumi A, Kadokura H, Kikkawa M, Inaba K
Cryo-EM analysis provides new mechanistic insight into ATP binding to Ca2+-ATPase SERCA2b
EMBO J. (2021) DOI: 10.15252/embj.2021108482