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

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