Faculty Profiles - TERADA, Tomoki

Presentations -

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Construction of a simulation model which reproduces the single molecule experiment on biased Brownian motion of myosin head

Kenshiro Kaneko, Tomoki P. Terada

2024.9.30

ミオシンのアクチンに沿ったバイアスブラウン運動とその筋収縮における役割 Invited

寺田智樹

第13回分子モーター討論会 2024.9.30 分子モーター討論会

Construction of a simulation model which reproduces the single molecule experiment on biased Brownian motion of myosin head

Kenshiro Kaneko, Tomoki P. Terada

The Physical Society of Japan 2024 Annual Meeting 2024.9.18 The Physical Society of Japan

Optimizing the intramolecular interactions in the chameleon model focusing on the conformational transition of adenylate kinase

Tomoki P. Terada

The 24th Annual Meeting of the Protein Science Society of Japan 2024.6.13 Protein Science Society of Japan

Conformational transition and unfolding of adenylate kinase studied by chameleon model International conference

Tomoki P. Terada

The 61th Annual Meeting of the Biophysical Society of Japan 2023.11.15

The effect of biased Brownian motion on the macroscopic properties of muscle contraction in the simulation model of actomyosin interaction International conference

Shunta Oda, Tomoki P. Terada

The 61th Annual Meeting of the Biophysical Society of Japan 2023.11.16

A study on the role of biased Brownian motion in the simulation of muscle contraction

Shunta Oda, Tomoki P. Terada

2023.9.16 The Physical Society of Japan

Conformational transition and unfolding of adenylate kinase studied by chameleon model

Tomoki P. Terada, Eiichiro Yamaoka

2023.7.7 Protein Science Society of Japan

Construction of six-state model of muscle contraction with switched free energy landscape and power stroke

Shunta Oda, Tomoki P. Terada

The 60th Annual Meeting of the Biophysical Society of Japan 2022.9.29 The Biophysical Society of Japan

Testing cooperativity of chameleon model by sigmoidal oxygen binding curve of hemoglobin

Itsuki Yoshida, Tomoki P. Terada

The 60th Annual Meeting of the Biophysical Society of Japan 2022.9.28 The Biophysical Society of Japan

Free energy landscape analysis of conformational transition of NtrC by chameleon model

Taisei Nagata, Masaki Sasai, Tomoki P. Terada

The 59th Annual Meeting of the Biophysical Society of Japan 2021.11.26 The Biophysical Society of Japan

Event date： 2021.11

Language：English Presentation type：Oral presentation (general)

Venue：Online Country：Japan

We study the conformational transition by coarse-grained molecular dynamics simulation. We use chameleon model, an extended model of Go-like model with which we can calculate the free energy landscape of confrontational transitions (Terada et al., J. Phys. Chem. B 117, 12864 (2013)). We focus on the NtrC receiver domain which exhibits allosteric transition with the register shift of anα-helix. The chameleon model was applied to NtrC and the simulation results showed a free energy landscape with two states corresponding to active and inactive states. Therefore, we performed a free energy landscape analysis of conformational transition of NtrC. Free energy landscape analysis shows that the α-helix rotates in the intermediate state between active and inactive states.

A study on the conformational transition of adenylate kinase by the chameleon model

Itsuki Yoshida, Masaki Sasai, Tomoki P. Terada

The 59th Annual Meeting of the Biophysical Society of Japan 2021.11.26 The Biophysical Society of Japan

Event date： 2021.11

Language：English Presentation type：Oral presentation (general)

Venue：Online Country：Japan

Chameleon model is the model for description of two-state conformational transition of proteins. In the model, the interaction between residues changes depending on how similar the environment around the residues is to one state and the other state. We applied the model to the conformational transition of adenylate kinase. We calculated the rates of conformational transition from the free energy difference between fully closed state and transition state which is the rate-limiting step of the enzymatic activity. We found that the temperature dependence of calculated conformational transition rates is similar to that of experimental enzymatic activity, showing that chameleon model gives a good approximation of free energy landscape of conformational transition.

A landscape-based view on the stepping movement of myosin VI International coauthorship

Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

Three-state model of muscle contraction with switched free energy landscapes and power stroke

Kaima Matsuda, Masaki Sasai, Tomoki P. Terada

Conformational transition of NtrC elucidated by the improvement of dihedral angle potential in chameleon model

Taisei Nagata, Masaki Sasai, Tomoki P. Terada

ミオシンVIの歩行メカニズムの自由エネルギーランドスケープ解析

寺田智樹, Qing-Miao Nie, 笹井理生

日本物理学会第75回年次大会

A landscape-based view on the stepping movement of myosin VI International conference

Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

64th Annual Meeting of the Biophysical Society

Effects of interhead connection on the stepping motion of myosin VI

Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

A landscape-based view on the stepping movement of myosin VI International conference

Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

Joint 12th EBSA, 10th ICBP-IUPAP Biophysics Congress

Free energy landscape for the Brownian motion of the leading head of myosin VI during the stepping motion Invited International conference

Tomoki P. Terada

The 2nd workshop on Advances in Theory and Computation of Complex Systems - Biological Systems

Free energy landscape for the Brownian motion of the leading head of myosin VI during the stepping motion

Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

The 56th Annual Meeting of The Biophysical Society of Japan

ミオシンの構造変化とバイアスブラウン運動の協調的関係 Invited

寺田智樹

第三回CUTEシンポジウム：コンピュータ化学 -計算科学と実験化学との接点-

ミオシンのバイアスブラウン運動を自由エネルギーランドスケープから考える Invited

寺田　智樹

自然科学研究機構計算科学研究センタースーパーコンピュータワークショップ“複雑な研究対象へと挑戦する計算分子科学“

ミオシンのバイアスブラウン運動を自由エネルギーランドスケープから考える Invited

寺田　智樹

第5回分子モーター討論会

Coupling between phosphorylation rhythm and ATP hydrolysis rate in KaiC protein studied by stochastic simulation Invited International conference

Tomoki P. Terada

2015 International Workshop on Computational Science and Engineering

Stochastic simulation of coupling between phosphorylation rhythm and ATP hydrolysis in KaiC protein

Tomoki P. Terada, Kenju Narita, Masaki Sasai

The Physical Society of Japan 2015 Spring Meeting

Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin

Tomoki P. Terada,Qing-Miao Nie,Akio Togashi,Takeshi N. Sasaki,Mitsunori Takano,Masaki Sasai

The Physical Society of Japan 2014 Autumn Meeting

Stochastic modeling of the interplay between ATPase activity and structural transition in KaiC proteins Invited International conference

Tomoki P. Terada

Joint Annual Meeting of the Japanese Society for Mathematical Biology and the Society for Mathematical Biology 2014 (JSMB/SMB 2014)

ES細胞の細胞運命決定における非平衡性の役割 Invited

寺田智樹

明星大学セミナー

The role of non-adiabaticity in cell-fate decision of ES cells Invited International conference

Tomoki P. Terada

The 3rd International Workshop on "Multiscale Characterizations of Biological Systems: From Molecules to Networks"

二重最適化問題としての蛋白質フォールディングとその進化 Invited

寺田智樹

第1回協定講座シンポジウム「計算アルゴリズムと化学・生物学の融合」

ゆらぎが決める蛋白質の多様な機能 Invited

寺田智樹

生物に学ぶ柔軟なシステムの探索：　ゆらぎと多様性をキーワードとして

The chameleon model: a novel approach to conformational transitions of proteins International conference

Tomoki P. Terada, Takahiro Yamashita, Shogo Yokota, Toru Kimura, Masaki Sasai

The 1st KIAS Conference on Subcellular Dynamics

Chameleon model: A Novel Approach to Conformational Transitions of Proteins Invited International conference

Tomoki P. Terada

The 2nd International Workshop on Multiscale Characterizations of Biological Systems: From Molecules to Networks

Chameleon model: A Novel Approach to Conformational Transitions of Proteins Invited International conference

Tomoki P. Terada

Third Korea-Japan Seminars on Biomolecular Sciences: - Experiments and Simulations

タンパク質の構造転移メカニズムのカメレオンモデルによる理解 Invited

寺田智樹

生物物理の未来研究会

Event date： 2010.9

Language：Japanese Presentation type：Oral presentation (invited, special)

Venue：名古屋大学ベンチャービジネスラボラトリーベンチャーホール Country：Japan

タンパク質が熱揺らぎで構造転移をすることが、最近の一分子測定やNMRなどの実験からわかってきた。われわれは、構造転移を記述しうる粗視化モデル相互作用として、局所的相互作用がその周囲の変化に合わせて変化すると仮定するカメレオンモデルを提唱している。このモデルをアデニル酸キナーゼに対して適用した結果、実験で観測された二状態的な構造転移が再現されるとともに、モデルで計算された構造転移速度の温度変化が実測された酵素反応速度の温度変化とよく対応することがわかった。これらの結果は、カメレオンモデルが構造転移の

カメレオンモデルによるタンパク質の二状態的構造転移の自由エネルギーランドスケープ解析 Invited

寺田智樹

第１０回日本蛋白質科学会年会

Event date： 2010.6

Language：Japanese Presentation type：Oral presentation (invited, special)

Country：Japan

タンパク質がリガンド結合に伴い構造を変えることは長い間知られてきたが、近年は一定条件のもとで熱揺らぎで起こる構造転移に対しても、一分子実験やNMRなどによる実験的な特徴づけが進んできた。理論的立場からは、フォールディング研究における郷モデルの延長として、二つの結晶構造をともにエネルギー的に安定化する実効的相互作用が提唱されてきたが、二状態的な自由エネルギーランドスケープが得られるということ以上には実験事実との対応付けは行われていない。われわれはそれらの研究とは異なり、局所的相互作用がその周囲の変化

Takano-Terada-Sasai model Invited

Contribution of hydrophobic and electrostatic interactions in the biased motion of myosin head along actin filament

45th Annual Meeting of the Biophysical Society of Japan

Event date： 2007.12

Language：Japanese Presentation type：Poster presentation

Country：Japan

We have simulated the motion of myosin head along the actin filament with coarse-grained molecular dynamics with introduceing the sequence-dependent water-mediated potential. This potential have three variants depending on the degree of unfolding of each protein prior to binding. The simulation with this potential elucidates the contribution of hydrophobic and electrostatic interactions in the biased motion as well as the importance of coupled folding and binding.

ミオシン滑り運動とカメレオンGoモデル Invited

寺田智樹

次世代生命体統合・分子スケール　秋のミニ集会

Molecular dynamics simulation of biased motion of myosin head along actin filament International conference

Discussions on Theory and simulation of biomolecular systems

Molecular dynamics simulation of biased motion of myosin head along actin filament International conference

Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan

アクトミオシンの粗視化モデルによる分子動力学計算－レバーアーム模型ではない何かを求めて－

寺田智樹

CRESTチームミーティング

アクトミオシンの粗視化モデルによる分子動力学計算III

寺田智樹、笹井理生

日本生物物理学会第４３回年会

蛋白質のやわらかさとミオシンの一方向的な滑り運動 Invited

笹井理生、寺田智樹

生体分子とゆらぎ研究会2005

アクトミオシンの粗視化モデルによる分子動力学計算II

寺田智樹、笹井理生

日本生物物理学会第４２回年会

アクトミオシンの粗視化モデルによる分子動力学計算

寺田智樹、笹井理生

日本生物物理学会第４１回年会

アクトミオシンの滑り運動の一分子観測に対する新しい視点 Invited

寺田智樹

日本生物物理学会第４１回年会

アクトミオシンの一方向的な滑り運動とエネルギーランドスケープ理論 Invited

寺田智樹

第３回日本蛋白質科学会

Conformational change of actomyosin complex drives the multiple stepping movement Invited

Dynamics and Function of Nano-Biomechines

Conformational change of actomyosin complex drives the multiple stepping movement International conference

The 16th Symposium of the Protein Society

アクトミオシンの滑り運動の一方向性は構造変化の一方向性とカップルしている

寺田智樹、笹井理生、四方哲也

第２回日本蛋白質科学会

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