Hidetoshi Kono

Profile Information

Affiliation: Group Leader, National Institutes for Quantum and Radiological Science and Technology

ORCID ID: https://orcid.org/0000-0001-5729-8707
J-GLOBAL ID: 200901009532752634
researchmap Member ID: 5000092747

Research Interests

protein-DNA; nucleosome; protein design; DNA-binding protein; molecular modeling

Research Areas

Awards

Sep, 2013

第2回BIOPHYSICS論文賞, 日本生物物理学会

Shoichi Metsugi, Atsuko Uenoyama, Jun Adan-Kubo, Makoto Miyata, Kei Yura, Hidetoshi Kono, Nobuhiro Go
2002

Oxford Univ. Press Bioinformatics Prise

Sarai, A, Gromiha, M.M, Selvaraj, S, Sieber, J. G, Prabakaran, P, H. Kono

Papers

149

Designer Adaptor Proteins for Functional Conversion of Peptides to Small-Molecule Ligands toward In-Cell Catalytic Protein Modification.

Akiko Fujimura, Hisashi Ishida, Tamiko Nozaki, Shuhei Terada, Yuto Azumaya, Tadashi Ishiguro, Yugo R Kamimura, Tomoya Kujirai, Hitoshi Kurumizaka, Hidetoshi Kono …

ACS central science, 9(11) 2115-2128, Nov 22, 2023
Structural and Dynamical Changes of Nucleosome upon GATA3 Binding.

Hisashi Ishida, Atsushi Matsumoto, Hiroki Tanaka, Aya Okuda, Ken Morishima, Paul A Wade, Hitoshi Kurumizaka, Masaaki Sugiyama, Hidetoshi Kono

Journal of molecular biology, 168308-168308, Oct 5, 2023
Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Junichi Higo, Kota Kasahara, Gert-Jan Bekker, Benson Ma, Shun Sakuraba, Shinji Iida, Narutoshi Kamiya, Ikuo Fukuda, Hidetoshi Kono, Yoshifumi Fukunishi …

Scientific Reports, 12(1), Aug 13, 2022 Peer-reviewed
RNAPII driven post-translational modifications of nucleosomal histones

Justin Chan, Amarjeet Kumar, Hidetoshi Kono

Trends in Genetics, May, 2022 Peer-reviewedLast authorCorresponding author
Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach.

Yasuhiro Yunoki, Atsushi Matsumoto, Ken Morishima, Anne Martel, Lionel Porcar, Nobuhiro Sato, Rina Yogo, Taiki Tominaga, Rintaro Inoue, Maho Yagi-Utsumi …

Communications biology, 5(1) 184-184, Mar, 2022 Peer-reviewedCorresponding author
HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks

Effi Haque, Aamir Salam Teeli, Dawid Winiarczyk, Masahiko Taguchi, Shun Sakuraba, Hidetoshi Kono, Paweł Leszczyński, Mariusz Pierzchała, Hiroaki Taniguchi

Genes, Feb 24, 2022 Peer-reviewed
Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex

Shun Sakuraba, Bert L. de Groot, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono

PLOS Computational Biology, 18(1) e1009804-e1009804, Jan 19, 2022 Peer-reviewedLast author
Interplay among transacting factors around promoter in the initial phases of transcription.

Amarjeet Kumar, Justin Chan, Masahiko Taguchi, Hidetoshi Kono

Current opinion in structural biology, 71 7-15, Dec, 2021 Peer-reviewedInvitedLast authorCorresponding author
Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

Ko Sato, Amarjeet Kumar, Keisuke Hamada, Chikako Okada, Asako Oguni, Ayumi Machiyama, Shun Sakuraba, Tomohiro Nishizawa, Osamu Nureki, Hidetoshi Kono …

Nature Communications, 12(1) 6605-6605, Dec, 2021 Peer-reviewed
The N-terminal Tails of Histones H2A and H2B Adopt Two Distinct Conformations in the Nucleosome with Contact and Reduced Contact to DNA

Hideaki Ohtomo, Jun-ichi Kurita, Shun Sakuraba, Zhenhai Li, Yasuhiro Arimura, Masatoshi Wakamori, Yasuo Tsunaka, Takashi Umehara, Hitoshi Kurumizaka, Hidetoshi Kono …

Journal of Molecular Biology, 433(15) 167110-167110, Jul, 2021 Peer-reviewed
NRF2 DLG Domain Mutations Identified in Japanese Liver Cancer Patients Affect the Transcriptional Activity in HCC Cell Lines

Effi Haque, Magdalena Śmiech, Kamila Łuczyńska, Marie France Bouchard, Robert Viger, Hidetoshi Kono, Mariusz Pierzchała, Hiroaki Taniguchi

International Journal of Molecular Sciences, 22(10) 5296-5296, May 18, 2021 Peer-reviewed
Sequence-dependent Hydration Water Dynamics of Dodecameric DNA

Hiroshi Nakagawa, Yoshiteru Yonetani, Kenji Nakajima, Seiko Ohira-Kawamura, Tatsuya Kikuchi, Yasuhiro Inamura, Mikio Kataoka, Hidetoshi Kono

Proceedings of the 3rd J-PARC Symposium (J-PARC2019), Mar 26, 2021 Peer-reviewedLast author
Emerging BRAF Mutations in Cancer Progression and Their Possible Effects on Transcriptional Networks

Magdalena Śmiech, Paweł Leszczyński, Hidetoshi Kono, Christopher Wardell, Hiroaki Taniguchi

Genes, 11(11) 1342-1342, Nov 12, 2020 Peer-reviewed
Structural basis for designing an array of engrailed homeodomains

Tomoko Sunami, Yu Hirano, Taro Tamada, Hidetoshi Kono

Acta Crystallographica Section D Structural Biology, 76(9) 824-833, Sep 1, 2020 Peer-reviewedCorresponding author
Structural Studies of Overlapping Dinucleosomes in Solution

Hidetoshi Kono

Biophysical Journal, 118(9) 2209-2219, May, 2020 Peer-reviewed
Heterochromatin protein 1 (HP1): interactions with itself and chromatin components

Hidetoshi Kono

Biophysical Reviews, Apr, 2020 Peer-reviewed
Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation

Hidetoshi Kono

Nature Communications, Dec, 2019 Peer-reviewed
Balance between DNA‐binding affinity and specificity enables selective recognition of longer target sequences in vivo

Tomoko Sunami, Hidetoshi Kono

Protein Science, Aug 6, 2019 Peer-reviewed
Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

Hidetoshi Kono

Biophysics and Physicobiology, 2019 Peer-reviewed
Investigating the Influence of Arginine Dimethylation on Nucleosome Dynamics Using All-Atom Simulations and Kinetic Analysis

Zhenhai Li, Hidetoshi Kono

The Journal of Physical Chemistry B, 122(42) 9625-9634, Oct 25, 2018 Peer-reviewed

Misc.

The Advantage of Small-angle Neutron Scattering Revealed through Analyzing the Overall Structure of a Fully Assembled Complex in Circadian Clock

柚木康弘, 松本淳, 守島健, MARTEL Anne, PORCAR Lionel, 佐藤信浩, 與語理那, 與語理那, 與語理那, 富永大輝 …

波紋, 32(4), 2022
最先端の研究開発量子科学技術研究開発機構第4回「量子生命科学」の発進

藤巻秀, 五十嵐龍治, 高草木洋一, 安達基泰, 横谷明徳, 玉田太郎, 河野秀俊, 鹿園直哉, 今岡達彦, 赤松憲 …

ΑΤΟΜΟΣ, 61(6) 477‐481, Jun 1, 2019
Distinct Roles of H3 and H2A Tails in Linker DNA Dynamics

Zhenhai Li, Jinzen Ikebe, Shun Sakuraba, Hidetoshi Kono

BIOPHYSICAL JOURNAL, 112(3) 373A-373A, Feb, 2017
The Free-Energy Landscape of the di-Nucleosome: A Critical Role of the H4 Tails for the Nucleosome-Nucleosome Conformation

Hisashi Ishida, Hidetoshi Kono

BIOPHYSICAL JOURNAL, 112(3) 216A-216A, Feb, 2017
Conformational Sampling of Unmodified and Acetylated H3 Histone Tails on a Nucleosome by All-Atom Model Molecular Dynamics Simulations

Jinzen Ikebe, Shun Sakuraba, Hidetoshi Kono

BIOPHYSICAL JOURNAL, 108(2) 540A-541A, Jan, 2015
Free Energy Profiles for Nucleosomal DNA Unwrapping

Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida

BIOPHYSICAL JOURNAL, 108(2) 73A-73A, Jan, 2015
29pAA-1 How do DNA-binding proteins find their target site? Insight from molecular dynamics free-energy calculations

Yonetani Yoshiteru, Kono Hidetoshi

Meeting abstracts of the Physical Society of Japan, 69(1) 413-413, Mar 5, 2014
Dissociation Free-Energy Profiles of Specific and Non-Specific DNA-Lac Repressor Complexes: Adaptive Biasing Force Molecular Dynamics Study

Yoshiteru Yonetani, Hidetoshi Kono

BIOPHYSICAL JOURNAL, 106(2) 70A-70A, Jan, 2014
Adaptive Lambda Square Dynamics Simulation: An Efficient Conformational Sampling Method for Biomolecules

Jinzen Ikebe, Shun Sakuraba, Hidetoshi Kono

BIOPHYSICAL JOURNAL, 106(2) 405A-405A, Jan, 2014
20pAB-12 Free energy profiles for DNA-protein dissociation protess : Adaptive-biasing force molecular dynamics calculation

Yonetani Yoshiteru, Kono Hidetoshi

Meeting abstracts of the Physical Society of Japan, 67(2) 339-339, Aug 24, 2012
24pBF-11 What determines water residence times at the surface of biomolecules?

Yonetani Yoshiteru, Kono Hidetoshi

Meeting abstracts of the Physical Society of Japan, 67(1) 399-399, Mar 5, 2012
3PS026 Automatic similarity identification of 2D diffraction patterns with noisy background for 3D coherent x-ray diffractive imaging(The 50th Annual Meeting of the Biophysical Society of Japan)

Tokuhisa Atsushi, Joti Yasumasa, Kono Hidetoshi, Go Nobuhiro

Seibutsu Butsuri, 52 S150, 2012
Local Conformational Changes of Proteins in DNA Interfaces

Tomoko Sunami, Hidetoshi Kono

BIOPHYSICAL JOURNAL, 102(3) 72A-72A, Jan, 2012
21pJF-9 What determines water lifetimes at the surface of biomolecules?

Yonetani Yoshiteru, Kono Hidetoshi

Meeting abstracts of the Physical Society of Japan, 66(2) 309-309, Aug 24, 2011
Free Energy Profiles for Nucleosome Position Changes

Hidetoshi Kono, Naoko Kanaeda, Hisashi Ishida

BIOPHYSICAL JOURNAL, 100(3) 66-66, Feb, 2011
24pTG-2 Theoretical sturdy for single bio-molecule imaging by using XFEL

Tokuhisa A., Taka J., Kono H., Go N.

Meeting abstracts of the Physical Society of Japan, 65(2) 325-325, Aug 18, 2010
23aTG-8 Sequence dependent dynamics of hydration water molecules in the minor groove of DNA

Yonetani Yoshiteru, Kono Hidetoshi

Meeting abstracts of the Physical Society of Japan, 65(2) 312-312, Aug 18, 2010
DNAの水和とダイナミクスの塩基配列依存性, DNA -タンパク質, DNA－低分子認識の理解に向けて

米谷佳晃, 河野秀俊

メディカルバイオ, 9月別冊 66, 2010
3P-069 Theory of single molecule imaging by X-ray free-electron laser(Protein:Measurement & Analysis,The 47th Annual Meeting of the Biophysical Society of Japan)

Tokuhisa Atsushi, Taka Junichiro, Kono Hidetoshi, Go Nobuhiro

Seibutsu Butsuri, 49 S162, 2009
22aWB-6 Relationship between DNA conformational fluctuation and hydration

Yonetani Yoshiteru, Fujii Satoshi, Sarai Akinori, Kono Hidetoshi, Go Nobuhiro

Meeting abstracts of the Physical Society of Japan, 63(2) 323-323, Aug 25, 2008

Research Projects

ヌクレオソーム高次構造とダイナミクスの解析によるクロマチン潜在能の解明

科学研究費助成事業, 新学術領域研究(研究領域提案型), 日本学術振興会, Jun, 2018 - Mar, 2023

胡桃坂仁志, 杉山正明, 河野秀俊
International research network for chromatin structure, dynamics, and function

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Japan Society for the Promotion of Science, Nov, 2015 - Mar, 2018

Kurumizaka Hitoshi, OBUSE Chikashi, HARAGUCHI Tokuko, YONEDA Yoshihiro, TOKUNAGA Makio, KONO Hidetoshi, SAITOH Noriko, OHKAWA Yasuyuki, HARATA Masahiko
Chromatin dynamics analysis using computer simulation

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Japan Society for the Promotion of Science, Jun, 2013 - Mar, 2018

Kono Hidetoshi, LI Zhenhai
Chromatin structure, dynamics, and function

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Japan Society for the Promotion of Science, Jun, 2013 - Mar, 2018

Kurumizaka Hitoshi, KIMURA Hiroshi, OBUSE Chikashi, HARAGUCHI Tokuko, YONEDA Yoshihiro, TOKUNAGA Makio, KONO Hidetoshi, SAITOH Noriko, OHKAWA Yasuyuki, HARATA Masahiko
Improvement of sequence specificity of DNA-binding protein using computational and experimental approaches

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2014 - Mar, 2017

KONO HIDETOSHI, SUNAMI Tomoko
Elucidation of information-processing mechanisms during transcription cycle using computational and information sciences

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Japan Society for the Promotion of Science, Jun, 2012 - Mar, 2017

NAKAMURA Haruki, KAMIYA Narutoshi, KONO Hidetoshi, KASAHARA Kota, IIDA Midori
ヌクレオソーム構造の自由エネルギープロファイル解析

科学研究費助成事業, 新学術領域研究(研究領域提案型), 日本学術振興会, Apr, 2011 - Mar, 2013

河野秀俊
シミュレーション計算によるヌクレオソーム構造形成の自由エネルギー地形解析

科学研究費助成事業, 新学術領域研究(研究領域提案型), 日本学術振興会, 2009 - 2010

河野秀俊
DNA配列に特異的に結合するタンパク質分子設計

科学研究費助成事業, 挑戦的萌芽研究, 日本学術振興会, 2009 - 2010

河野秀俊
Regulation of Gene Transcription Inferred From Transcription Factor Binding and Nucleosome Positioning

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, 2008 - 2010

KONO Hidetoshi, MATSUMOTO Atsushi
中性子散乱実験と分子動力学計算による蛋白質-DNA認識機構における水の挙動解析

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2007 - 2008

河野秀俊, 中川洋, 米谷佳晃
転写因子のターゲット部位予側にもとづく遺伝子の機能及び相互作用推定

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2004 - 2004

河野秀俊, KIM Thi Phuong Oanh
蛋白質の機能部位推定及びSNPによる機能変化の予側

科学研究費助成事業, 若手研究(B), 日本学術振興会, 2003 - 2004

河野秀俊
転写因子のターゲット部位予側からのゲノム機能推定

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2003 - 2003

河野秀俊
DNA結合蛋白質の機能性cavityと立体構造安定性

科学研究費助成事業, 特定領域研究(A), 日本学術振興会, 1998 - 1998

皿井明倫, 緒方一博, 斎藤稔, 森井尚之, GROMIHA Mich, 河野秀俊
hydration around DNA/protein
de novo design of proteins
DNA-binding protein
protein-DNA recognition

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