Fumiko Takagi
University of Tokyo
Network
Latest external collaboration on country level. Dive into details by clicking on the dots.
Publication
Featured researches published by Fumiko Takagi.
Proteins | 2015
Ryo Kanada; Fumiko Takagi; Macoto Kikuchi
Molecular motors such as kinesin regulate affinity to a rail protein during the ATP hydrolysis cycle. The regulation mechanism, however, is yet to be determined. To understand this mechanism, we investigated the structural fluctuations of the motor head of the single‐headed kinesin called KIF1A in different nucleotide states using molecular dynamics simulations of a Gō‐like model. We found that the helix α4 at the microtubule (MT) binding site intermittently exhibits a large structural fluctuation when MT is absent. Frequency of this fluctuation changes systematically according to the nucleotide states and correlates strongly with the experimentally observed binding affinity to MT. We also showed that thermal fluctuation enhances the correlation and the interaction with the nucleotide suppresses the fluctuation of the helix α4 . These results suggest that KIF1A regulates affinity to MT by changing the flexibility of the helix α4 during the ATP hydrolysis process: the binding site becomes more flexible in the strong binding state than in the weak binding state. Proteins 2015; 83:809–819.
Computer Physics Communications | 2011
Shigenori Matsumoto; Fumiko Takagi; Takashi Shimada; Nobuyasu Ito
Abstract We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models.
Biophysical Journal | 2007
Fumiko Takagi; Macoto Kikuchi
arXiv: Biomolecules | 2006
Fumiko Takagi; Macoto Kikuchi
Biophysical Journal | 2016
Macoto Kikuchi; Ryo Kanada; Fumiko Takagi
Meeting abstracts of the Physical Society of Japan | 2012
Fumiko Takagi; Nobuyasu Ito
生物物理 | 2011
Fumiko Takagi; Macoto Kikuchi; Nobuyasu Ito
Seibutsu Butsuri | 2011
Fumiko Takagi; Macoto Kikuchi; Nobuyasu Ito
生物物理 | 2010
Shigenori Matsumoto; Fumiko Takagi; Takashi Shimada; Nobuyasu Ito
生物物理 | 2010
Fumiko Takagi; Macoto Kikuchi; Nobuyasu Ito