Molecular Biophysics

Protein structure, dynamics - Biophysical methods, Bioimaging, Proteomics, Computational simulations in Molecular & Cellular Biology

Our Research

Through analysis of the dynamic structural properties of proteins, we will elucidate the functional role of fluctuations in protein structures. In particular, we are conducting research focusing on the elucidation of new functions of intrinsically disordered regions (IDRs). The characteristic of the research carried out in this laboratory is to proceed with the development of original research based on the development of new structural analysis technology.

CURRENT PROJECTS

Tteam is currently involved in projects related to liquid-liquid phase separation, chirality, allostery and related biological phenomena, through a variety of experimental and computational methods.

Proteomics Analysis of Biomolecular Condensates

Proteins harboring intrinsically disordered regions (IDRs) form biomolecular condensates through liquid-liquid phase separation (LLPS) in live cells. The liquid-like granular condensates are composed of variety of proteins and RNAs. By choosing the stress granule and ALS-related cytoplasmic granules as models, our group tries to reveal the time-dependent change in the constitution of those biomolecular condensates. The project runs in collaboration with Prof. Rhee of Seoul National University, Korea.

Live Imaging of Biomolecular Condensates with Electron Microscopy

In collaboration with Dr. Ogura (National Institute of Advanced Industrial Science and Technology, Tsukuba), our group is tackling to image the biomolecular condensates in live cells at nano-scale resolution. The project aims to unveil how various biomolecules assemble to generate condensates.

Exploring the Molecular Mechanism of Protein Condensation via Liquid-Liquid Phase Separation (LLPS)

Proteins with the intrinsically disordered regions (IDRs) mediate biomolecular granulation via liquid-liquid phase separation (LLPS). We explore the molecular mechanism of protein granulation with advanced NMR spectroscopy combined with molecular biology and theoretical simulation like molecular dynamics simulation. The research outcomes will unveil the pathogenic mechanisms of neurodegenerative diseases, including ALS and Alzheimer’s diseases.

Chromatin Structure and Dynamics in Live Cells with Electron Microscopy and Mathematical Models

DNA is packed in the cell nucleus as chromatin fibers comprising nucleosomes (protein-DNA complex). Gene regulation in the cell nucleus requires a dynamic structural change of chromatin. In collaboration with Prof. Awazu and Prof. Ueno in the university, our group explores how the chromatin structure dynamics engage in gene regulation with multimodal approaches using light microscopy, electron microscopy, and mathematical modeling to integrate the experimental observations.

Theoretical basis of allostery in enzymatic catalysis

By combining Nuclear Magnetic Resonance experiments with Computational Modeling, we are exploring the mechanism of allostery in dihydrofolate reductase (DHFR) as revealed by a novel mutation. Via Molecular Dynamics (MD) simulations, we explore changes to changes in dynamics that may explain changes in catalytic activity.

STAFF

Led by Prof. Shinichi Tate

Shin-ichi Tate

Professor

Kyota Yasuda

Assistant Professor

Sandhya P. Tiwari

Assistant Professor

PUBLICATIONS

  • Ichinose,J., Oba,K., Arase,Y., Kaneshiro,J., Tate,S., and Wanatabe,T.M., "Quantitative prediction of rice starch digestibity using Raman spectroscopy and multivariate calibration analysi", Food Chem. in press (2023)

  • Dasgupta,B. and Tiwari,S.P.,“Explicit versus implicit cnsideration of binding partners in protein-protein complex to elucidate intrinsic dynamics”, Biophysical Reviews, in press (2022)

  • 「タンパク質の揺らぎ・反応」高圧力の科学・技術事典（監修：日本高圧力学 会，編集：入舩徹男，加藤稔，木村佳文，近藤正，清水克哉，関根利守，長谷川正，舟越 賢一，保科貴亮，松木均）朝倉書店 (2022)

  • Liao,Z., Oyama,T., Kitagawa,Y., Katayanagi,K., Morikawa,K., and Oda,M. “Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography”, Acta Cryst., D78, 390-398 (2022)

  • Yasuda, K., Watanabe, T.M., Kang, M., Seo, J.K., Rhee, H., Tate, S., "Valosin-containing protein (VCP) regulates the stability of fused in sarcoma (FUS) granules in cells by changing ATP concentrations", FEBS Lett., 596, 1412-1423 (2022)

  • Sato, K., Sakai, M., Ishii, A., Maehata, K., Takada, Y., Yasuda, K., Kotani, T., "Identification of embryonic RNA granules that act as sites of mRNA translation after changing their physical properties", iScience, 25, 104344 (2022)

  • 安田恭大，楯　真一　「FUS液液相分離の機能と細胞内相分離制御機構」（Function and regulatory mechanism of intracellular FUS-LLPS）　細胞　54（8），448－451（2022）

  • Moritsugu,K., Yamamoto,N., Yonezawa,Y., Tate,S., and Fujisaki,H. “Path ensembles for Pin1-catalized cis/trans isomerization of a substrate calculated by weighted ensemble simulations”, J. Chem. Theory Comput., 17, 2522-2529 (2021)

  • Kondo,K., Ikura,T., Homma,H., Liu,S., Kawasaki,R., Huang,Y., Ito,N., Tate,S., and Okazawa,H. "Hepta-Histidine Inhibits Tau Aggregation" ACS Chemical Neurosci. 12,3015-3027 (2021)

  • Fujimoto,H., Shimoyama,D., Katayanagki,K., Kawata,N., Hirao,T., and Haino,T. “Negative cooperativity in guest binding of a ditopic self-folding biscavitand”, Org. Lett., 23, 621706221 (2021)

  • Tiwari,S.P., Tama,F., and Miyashita,O.,"Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns" J. Chem. Inf. Model. 61, 4108-4119 (2021)

  • 楯　真一，タンパク質天然変性領域が実現するヌクレオソーム結合能の「超高感度応答性」機構， 生物物理, 61, 312-315（2021)

  • 大前　英司「Unfolding of Proteins タンパク質のアンフォールディング」, 熱測定, 48, 72-77 (2021)

  • Andersen, C. B., Yoshimura, Y., Nielsen, J., Otzen, D. E. & Mulder, F. A. A., "How epigallocatechin gallate binds and assembles oligomeric forms of human alpha-synuclein" J. Biol. Chem. 296, 100788 (2021)

  • Yoshimura, Y., So, M. & Miyanoiri, Y., "Carbonyl 13C-detect solution-state protein NMR experiments to circumvent amide-solvent exchange broadening: Application to β2-microglobulin", Biochim. Biophys. Acta. 1869, 140593 (2021)

  • Kawasaki,R. and Tate,S. “Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments”, International Journal of Molecular Science. 21, 3920 (2020)

  • Aoki,D., Awazu, A., Fujii,M., Uewaki,J., Hashimoto, M., Tochio,N., Umehara,T., and Tate,S. “Ultrasensitive Change in Nucleosome Binding by Multiple Phosphorylations to the Intrinsically Disordered Region of the Histone Chaperone FACT”, J.Mol.Biol. 432, 4637-4657 (2020)

  • Ohmae, E., Miyashita, Y., and Kato, C. “Functional, structural, and thermodynamic characteristics of enzymes from deep-sea microorganisms.” Microbial Catalysts Volume 1 (Eds. S. M. Abdel-Aziz, N. Garg, A. Aeron, C. K. Jha, S. C. Nayak, and V. K. Bajpai), Chapter 12, pp. 325-343, Nova Science Publisher, (2019)

  • 大前英司「高圧力が酵素に及ぼす影響―深海微生物由来酵素の高圧力適応機構―」化学と生物, 58, 635-639 (2020)

  • Yoshimura, Y. & Mulder, F. A. A.,"Sensitive and simplified: a combinatorial acquisition of five distinct 2D constant-time 13C−1H NMR protein correlation spectra" J. Biomol. NMR. 74, 695-706 (2020)

  • Ohta,T., Yamada,R., Fujita,S., Takahata,T., Shiba,K., Machida,S., and Tate,S. “DOPG small unilamellar vesicles function as nano-carriers targeting the clustered lectin-like oxidized LDL receptor (LOX-1) on the cell surface, J. Drug Delivery Sci. and Tech., 51, 327-336 (2019)

  • Ito,H., Sugawara,T., Shinkai,S., Mizukawa,S., Kondo,A., Senda,H., Sawai,K., Suzuki, S.,Takaine,M., Yoshida,S., Imamura,H., Kitamura,K., Namba,T., Tate,S., and Ueno,M. “Spindle pole body movement is affected by glucose and ammonium chloride in fission yeast”, BBRC, 511, 820825 (2019)

  • Born,A., Nichols,P.J., Henen,M.A., Chi,C.N., Strotz,D., Bayer,P., Tate,S., Peng,J.W., Vogeli,B."Backbone and side-chain chemical shift assignments of full-length, apo, human Pin1, a phosphorprotein regulator with interdomain allostery" Biomol. NMR Assign., 13, 85-89 (2019)

  • David BG, Fujita H, Yasuda K, Okamoto K, Panina Y, Ichinose J, Sato O, Horie M, Ichimura T, Okada Y and Watanabe TM, “Linking substrate and nucleus via actin cytoskeleton in pluripotency maintenance of mouse embryonic stem cells”. Stem Cell Research, 41: 101614 (2019)

  • Moissoglu K*, Yasuda K*, Wang T*, Chrisafis G and Mili S, “Translational regulation of protrusion-localized RNAs involves silencing and clustering after transport”, eLife, 8: e44752, (2019). *equally contributed

  • Ikura,T., Tochio,N., Kawasaki,R., Matsuzaki,M., Narita,A., Kikumoto,M., Utsunomiya-Tate,N., Tate,S., and Ito,N."The trans isomer of Tau peptide is prone to aggregate, and the WW domain of Pin1 drastically decreases its aggregation" FEBS Lett., in press (2018)

  • Ohmae,E., Hamajima,Y., Nagae,T., Watanabe,N., and Kato,C. "Similar structural stabilities of 3-isopropylmalate dihydrogenases from the obligatory piezophlic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1" Biochim. Biophys. Acta, in press (2018)

  • Saito,M., Hiratoko,S., Fukuba,I., Tate,S., and Matsuoka,H., "Use of a right triable chip and its engraved shape as a transferrable x-y coordiante system from light microscopy to electron microscopy" Electrochemistry, 86, 6-9 (2018)

  • Umehara,K., Hoshikawa,M., Tochio,N., and Tate,S., "Substrate binding switches the conformation at the lychpin site in the substrate-binding domain of human Hsp70 to enable allosteric interdomain communication" Molecules, 23, 528 (2018)

  • Tate,S., "Protein structure and dynamics determination by residual anisotropic spin interactions" Experimental Approaches of NMR Spectroscopy (The Nuclear Magnetic Resonance Society of Japan Ed.), Springer (2018)

  • Tate,S., “Establishing a model to demonstrate physical and mathematical properties of chromatin fibres in fission yeast cells – Research in the molecular Biophysics Lab at Hiroshima University”, Impact, 89-91 (2018)

  • 大前英司「生命科学研究に用いられる高圧力実験装置の現状と今後の課題」高圧力の科学と技術 28巻1号, 31-37 (2018)

  • Mulder, F. A., Xue, M., Yoshimura, Y. & Kitahara, R., "How and why internal cavities destabilize proteins", The FASEB Journal. 32, 792.22-792.22 (2018)

  • Wang,J., Kawasaki,R., Uewaki,J., Rashid,A.U.R., Tochio,N., and Tate,S., "Dynamic allostery modulates catalytic activity by modifying hydrogen bonding network in the catalytic site of human Pin1" Molecules, 22, 992 (2017)

  • Yoshimura,Y., Oktaviani,N.A., Yonezawa,K., Kamikubo,H., and Mulder,F.A.A., "Unambiguous determination of protein arginine ionization states in solution by NMR spectroscopy" Angew. Chem. Int. Ed., 56, 239-242 (2017)

  • Nakamura,A., Tochio,N., Fuijoka,S., Ito,S., Kigawa,T., Shimada,Y., Matuoka,M., Yoshida,S., Kinoshita,T., Asami,T., Seto,H., "Molecular actions of two synthetic brassinosteroids, iso-carbaBL and 6-deoxoBL, which cause altered physiological activities between Arabidopsis and rice" PLoS One, 12, e0174015 (2017)

  • Makino,A., Abe,M., Ishitsuka,R., Murata,M., Kishimoto,T., Sakai,S., Hullin-Matuda,F., Shimada,Y., Inaba,T., Miyatake,H., Tanaka,H., Kurahashi,A., Pack,C.G., Ksai,R.S., Kubo,S., Schieber,N.L., Dohmae,N., Tochio,N., Hagiwara,K., Sasaki,Y., Aida,Y., Fujimori,F., Kigawa,T., Nishibori,K., Parton,R.G., Kusumi,A., Sako,Y., Anderluh,G., Yamashita,M., Kobayashi,T., Greimel,P., and Kobayashi,T., "A novel sphingomyelin/cholesterol domain-specific probe reveals the dynamics of the membrane domains during virus release and in Niemann-Pick type C" FASEB J., 31, 1301-1322 (2017)

  • Eguchi,Y., Okajima,T., Tochio,N., Inukai,Y., Shimizu,R., Ueda,S., Shinya,S., Kigawa,T., Fukamizo,T., Igarashi,M., and Utsumi,R., "Angucycline antibiotic waldiomycin recognizes common structural motif conserved in bacterial hitidine kinases" The Journal of Antibiotics, 70, 251-258 (2017)

  • Kuwasako,K., Nameki,N., Tsuda,K., Takahashi,M., Sato,A., Tochio,N., Inoue,M., Terada,T., Kigawa,T., Kobayashi,N., Shirouzu,M., Ito,T., Sakamoto,T., Wakamatsu,K., Guntert,P., TAkahashi,S., Ykoyama,S., and Muto,Y., "Solution structure of the first RNA recognition motif domain of human splicesomal protein SF3b49 and its mode of interaction with a SF3b145 fragment" Protein Sci., 26, 280-291 (2017)

  • Hiraishi,N., Maruno,T., Tochio,N., Sono,R., Otuki,M., Takatsuka,T., Tagami,J., and Kobayashi,Y., "Hesperidin interaction to collagen detected by physico-chemical techniques" Dental materials, 33, 33-42 (2017)

  • Oktaviani,N.A., Pool,T.J., Yoshimura,Y., Kamikubo,H., Scheek,R.M., Kataoka,M., Mulder,F.A.A., "Active-site Pka Determination for photoactive yellow protein rationalizes slow ground-state recovery" Biophy. J., 112, 2109-2116 (2017)

  • Miyashita,Y., Ohmae,E., Ikura,T., Nakasone,K., and Katayanagi,K., "Halophilic mechanism of the enzymatic function of moderately halophilic dihydropholate reductase from Haloarcula japonica strain TR-1" Extremophiles, 21, 591-602 (2017)

  • 楯　真一 "TALEタンパク質の超らせん運動とDNA配列認識"生物物理 57, 127-130 (2017)

  • 大前英司 "高圧処理による酵素の活性化と不活性化"食品と容器 58,404-410 (2017)

  • Yoshimura, Y., Holmberg, M. A., Kukic, P., Andersen, C. B., Mata-Cabana, A., Falsone, S. F., Vendruscolo, M., Nollen, E. A. A. & Mulder, F. A. A. (2017) MOAG-4 promotes the aggregation of α-synuclein by competing with self-protective electrostatic interactions, J Biol Chem. 292, 8269-8278

  • Yoshimura, Y., Oktaviani, N. A., Yonezawa, K., Kamikubo, H. & Mulder, F. A., "Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy", Angew Chem Int Ed Engl. 56, 239-242 (2017)

  • Oktaviani, N. A., Pool, T. J., Yoshimura, Y., Kamikubo, H., Scheek, R. M., Kataoka, M. & Mulder, F. A. A., "Active-Site pKa Determination for Photoactive Yellow Protein Rationalizes Slow Ground-State Recovery", Biophys. J. 112, 2109-2116 (2017)

  • Koefoed, L., Vase, K. H., Stenlid, J. H., Brinck, T., Yoshimura, Y., Lund, H., Pedersen, S. U. & Daasbjerg, K., "On the Kinetic and Thermodynamic Properties of Aryl Radicals Using Electrochemical and Theoretical Approaches", ChemElectroChem. 4, 3212-3221 (2017)

LATEST NEWS

Check our our latest activities!

Dec

17
2022
New publication in Biophysical Reviews

We discuss the implications of considering the dynamics of a protein in a protein-protein complex, as modelled implicitly and explicitly with methods dependent on elastic network models. We further propose how such an explicit consideration can be applied to understand critical protein-protein contacts that can be targeted in future studies.

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May

14
2022
New publication in iScience

Fertilized eggs begin to translate mRNAs at appropriate times and placements to control development, but how the translation is regulated remains unclear. Here, we found that pou5f3 mRNA encoding a transcriptional factor essential for development formed granules in a dormant state in zebrafish oocytes...

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June

24
2022
New publication in 月刊「細胞」2022年6月号

Topic from special edition・FUS液液相分離の機能と細胞内相分離制御機構（安田 恭大・楯 真一）

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CONTACT US

CONTACT INFO

  • Address:

    Molecular Biophysics Laboratory,

    Hiroshima University,

    Graduate School of Science,

    Mathematical Molecular Life Science,

    Faculty of Science / Department of Chemistry,

    1-3-1 Kagamiyama, Higashihiroshima City,

  • Mail Us: tate[at]hiroshima-u.ac.jp
  • Website: Faculty Profile