Akinori Kidera

Profile Information

Affiliation: Project Professor (Professor Emeritus), Graduate School of Medical Life Science, Yokohama City University

Degree: (BLANK)

J-GLOBAL ID: 200901093514214138
researchmap Member ID: 1000203366

External link: http://www.tsurumi.yokohama-cu.ac.jp/bioinfo/

経歴
京都大学大学院工学研究科博士課程修了工学博士
米国Cornell大学化学科博士研究員
京都工芸繊維大学工芸学部助手
蛋白工学研究所主任研究員
京都大学大学院理学研究科助教授
横浜市立大学大学院総合理学研究科教授
横浜市立大学大学院国際総合科学研究科生体超分子科学専攻専攻長
分子科学研究所理論分子科学研究系客員教授
理化学研究所次世代計算機科学研究開発プログラム次世代生命体シミュレーション研究推進グループ分子スケール研究開発チームチームリーダー（非常勤）
理化学研究所 HPCI計算生命科学推進プログラム副プログラムディレクター（非常勤）
横浜市立大学大学院生命医科学研究科研究科長

Research Interests

Research Areas

Life sciences / Biophysics /

Research History

Professor, Dean of Graduate School of Medical Life Science, Yokohama City University Graduate School of Medical Life Science

Papers

Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease.

Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi, Akinori Kidera

Journal of chemical information and modeling, 63(1) 240-250, Jan 9, 2023
Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA.

Akinori Kidera, Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi

Biophysical reviews, 14(6) 1473-1485, Dec, 2022
Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble

Akinori Kidera, Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi

Journal of Molecular Biology, 433(24) 167324-167324, Dec, 2021 Peer-reviewedLead authorCorresponding author
Molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain.

Keijun Kakihara, Kengo Asamizu, Kei Moritsugu, Masahide Kubo, Tetsuya Kitaguchi, Akinori Endo, Akinori Kidera, Mitsunori Ikeguchi, Akira Kato, Masayuki Komada …

Communications biology, 4(1) 1272-1272, Nov 8, 2021
Dynamic recognition and linkage specificity in K63 di-ubiquitin and TAB2 NZF domain complex

K. Moritsugu, H. Nishi, K. Inariyama, M. Kobayashi, A. Kidera

Scientific Reports, 8 16478, Nov, 2018 Peer-reviewed
Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion

K. Moritsugu, T. Terada, H. Kokubo, S. Endo, T. Tanaka, A. Kidera

Journal of Chemical Physics, 149(7) 072314, May, 2018 Peer-reviewed
Ionic scattering factors of atoms composing biological molecules

K.Yonekura, R. Matsuoka, Y. Yamashita, T. Yamane, M. Ikeguchi, A. Kidera, S. Maki-Yonekura

IUCrJ, 5(3) 348-353, Apr, 2018 Peer-reviewed
Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB

Y. Matsunaga, T. Yamane, T. Terada, K. Moritsugu, H. Fujisaki, S. Murakami, M. Ikeguchi, A. Kidera

ELife, 7 e31715, Mar, 2018 Peer-reviewed
Nature of self-diffusion in two-dimensional fluids

B. Choi, K. H. Han, C. Kim, P. Talkner, A. Kidera, E. K. Lee

New J. Phys., 19 123038, Dec, 2017 Peer-reviewed
Structureof the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance

Satoshi Ishiyama, Atsuya Nishiyama, Yasushi Saeki, Kei Moritsugu, Daichi Morimoto, Luna Yamaguchi, Naoko Arai, Rumie Matsumura, Toru Kawakami, Yuichi Mishima …

MOLECULAR CELL, 68(2) 350-+, Oct, 2017 Peer-reviewed
Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes

Kei Moritsugu, Tohru Terada, Akinori Kidera

JOURNAL OF PHYSICAL CHEMISTRY B, 121(4) 731-740, Feb, 2017 Peer-reviewed
Multiscale enhanced sampling for protein systems: An extension via adiabatic separation

Kei Moritsugu, Tohru Terada, Akinori Kidera

CHEMICAL PHYSICS LETTERS, 661 279-283, Sep, 2016 Peer-reviewed
Extended string-like binding of the phosphorylated HP1 alpha N-terminal tail to the lysine 9-methylated histone H3 tail

Hideaki Shimojo, Ayumi Kawaguchi, Takashi Oda, Nobuto Hashiguchi, Satoshi Omori, Kei Moritsugu, Akinori Kidera, Kyoko Hiragami-Hamada, Jun-ichi Nakayama, Mamoru Sato …

SCIENTIFIC REPORTS, 6 22527, Mar, 2016 Peer-reviewed
Itinerary profiling to analyze a large number of protein-folding trajectories

M. Ota, M. Ikeguchi, A. Kidera

Biophysics and Physicobiology, 18 295-304, 2016 Peer-reviewed
2PT134 Molecular dynamics simulation study of Lys48-linked diubiquitin in compact conformation(The 50th Annual Meeting of the Biophysical Society of Japan)

Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

Seibutsu Butsuri, 52 S127, 2012
3D1136 Molecular dynamics simulation study of diubiquitins : Analysis of ubiquitin-ubiquitin interactions(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

Seibutsu Butsuri, 51 S118-S119, 2011
2P039 Multidomain dynamics of a fatty acid β-oxidation multienzyme complex by molecular dynamics simulation(The 48th Annual Meeting of the Biophysical Society of Japan)

Furuta Tadaomi, Terada Tohru, Kidera Akinori

Seibutsu Butsuri, 50(2) S88-S89, 2010
1P-023 Molecular Dynamics Simulation Study of Diubiquitins with Different Linkages(Protein:Structure & Function, The 47th Annual Meeting of the Biophysical Society of Japan)

Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

Seibutsu Butsuri, 49 S67, 2009
3P-034 Molecular dynamics simulation of conformational change in a fatty acid β-oxidation multienzyme complex(Protein:Structure & Function,The 47th Annual Meeting of the Biophysical Society of Japan)

Furuta Tadaomi, Terada Tohru, Kidera Akinori

Seibutsu Butsuri, 49 S156, 2009
3P-018 Development of an exhaustive comparative simulation system(Protein:Structure,The 47th Annual Meeting of the Biophysical Society of Japan)

Terada Tohru, Furuta Tadaomi, Amemiya Takayuki, Kidera Akinori

Seibutsu Butsuri, 49 S153-S154, 2009

Misc.

A method for evaluating multicanonical potential function without iterative refinement: Application to conformational sampling of a globular protein in water

T Terada, Y Matsuo, A Kidera

JOURNAL OF CHEMICAL PHYSICS, 118(9) 4306-4311, Mar, 2003
Protein Dynamics Leading to Its Biological Functions

Kidera Akinori, Ikeguchi Mitsunoti

58(4) 246-253, 2003
A generalized form of the conserved quantity in constant-temperature molecular dynamics

Journal of Chemical Physics, 116, 33, 2002
Environmental Influence on Electron Scattering from a Molecule

Acta Crystallographica, A57, 518, 2001
Vibrational Energy Transfer in a Protein Molecule

PHysical Review Letter, 85, 3970, 2000
Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation

H Shirai, N Nakajima, J Higo, A Kidera, H Nakamura

JOURNAL OF MOLECULAR BIOLOGY, 278(2) 481-496, May, 1998
Canonical molecular dynamics of a protein in water by high-order decomposition of Liouville operator

Journal of Chemical Physics, 109 3276, 1998
Structural classification of CDR-H3 in antibodies

H Shirai, A Kidera, H Nakamura

FEBS LETTERS, 399(1-2) 1-8, Dec, 1996
Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides

NAKAJIMA N.

Journal of Physical Chemistry, 101(5) 817-824, 1996
Enhanced conformational sampling in Monte Carlo simulations of proteins : Application to a constrained peptide

Proceeding of National Academy of Science, U.S.A., 92(21) 9886-9889, 1995
DETERMINANTS OF PROTEIN SIDE-CHAIN PACKING

R TANIMURA, A KIDERA, H NAKAMURA

PROTEIN SCIENCE, 3(12) 2358-2365, Dec, 1994
Intrinsic nature of the three dimensional structure of protein as determined by distance geometry with good sampling properties

Journal of Biomolecular NMR, 3 19, 1993
Normal mode refinement : Crystallographic refinement of protein dynamic atructure (]G0001[) Theory and test by simulated diffraction data

Journal of Molecular Biology, 225(2) 457-475, 1992
Refinement of protein dynamic atructure : Normal mode refinement

Proceeding of National Academy of Science, U.S.A., 87(10) 3718-3722, 1990

Professional Memberships

Research Projects

Enhanced structural sampling for allosteric drug design

Grants-in-Aid for Scientific Research, Grant-in-Aid for Challenging Exploratory Research, Japan Society for the Promotion of Science, Apr, 2016 - Mar, 2019

Kidera Akinori, Moritsugu Kei, Ando Minami, Nishino Yoshihiko
Mechanism of signal transduction regulated by the interactions to cell membrane

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2016 - Mar, 2019

Kidera Akinori, Moritsugu Kei, Huang Bo
The role of the encounter complexes studied by molecular simulations of the protein complex formation processes.

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (A), Japan Society for the Promotion of Science, Apr, 2011 - Mar, 2015

AKINORI Kidera
タンパク質側鎖の平衡揺らぎと基質結合に伴う応答的運動

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

木寺詔紀
Identification of the relationship between protein structural changes and ligand binding on the basis of 3D protein structures

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

KIDERA Akinori, OTA Motonori
分子シミュレーションによる膜タンパク質の機能的ダイナミクスの研究

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

木寺詔紀, 池口満徳, 渕上壮太郎
分子シミュレーションによる蛋白質フォールディング・分子認識機構の解明

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2003 - 2007

池口満徳, 木寺詔紀, 渕上壮太郎
分子シミュレーションによる膜タンパク質の機能的ダイナミクスの研究

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2005 - 2006

木寺詔紀, 池口満徳, 渕上壮太郎
P型イオンポンプによる能動輪送機構の構造的解明

科学研究費助成事業, 学術創成研究費, 日本学術振興会, 2002 - 2006

豊島近, 杉田有冶, 津田岳夫, 木寺詔紀, 鈴木裕
Prediction of structure and function of protein complexes

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Priority Areas, Japan Society for the Promotion of Science, 2001 - 2004

KIDERA Akinori, IKEGUCHI Mitsunori, AKIO Kitao
水チャネルの選択性とその制御機構の解明

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2001 - 2004

光岡薫, 木寺詔紀, 藤本和, 藤吉好則
Decoding of genome function and evolution based on the 3D structures of proteins

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Priority Areas, Japan Society for the Promotion of Science, 2000 - 2004

GO Mitiko, TAKAHASHI Kenichi, SHIRAI Tsuyoshi, SODA Kunitsugu, YURA Kei
Structural and Informatics Basis of Channel Protein Interactions

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Priority Areas, Japan Society for the Promotion of Science, 2000 - 2004

NAKAMURA Haruki, NAKAJIMA Nobuyuki
Study of Vibrational Energy Transfer in Proteins

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, 2002 - 2003

KIDERA Akinori, IKEGUCHI Mitsunori
the maintenance and circulation of protein higher-order structural information and the evaluation of prediction information

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Priority Areas, Japan Society for the Promotion of Science, 2000 - 2002

GO Mitiko, NISHIKAWA Ken, MITAKU Shigeki, UMEYAMA Hideaki, KIDERA Akinori
蛋白質フォールディング研究の企画調査

科学研究費助成事業, 基盤研究(C), 日本学術振興会, 2001 - 2001

桑島邦博, 後藤祐児, 木寺詔紀, 新井宗仁, 平田文男, 中村春木
Energy Transfer in a Protein Molecule: From Chemical Reaction to Structural Change

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, 1999 - 2001

KIDERA Akinori, KINOSHITA Kengo, KITAO Akio
Free-R因子を上げずにより詳細な蛋白質モデルを構築するための結晶構造精密化法

科学研究費助成事業, 特定領域研究(A), 日本学術振興会, 2000 - 2000

木寺詔紀
プロテオーム時代の計算情報生物学

科学研究費助成事業, 基盤研究(C), 日本学術振興会, 1999 - 1999

郷通子, 中村春木, 美宅成樹, 西川建, 梅山秀明, 木寺紹紀
Program System for Protein Electron Crystallography

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, 1997 - 1999

KIDERA Akinori, ISHIDA Masahisa, MITSUOKA Kaoru, FUJIYOSHI Yoshinori, HIRAI Teruhisa