Fumiko Takagi

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How the Escherichia coli GroEL/ES chaperonin assists folding of a substrate protein remains to be uncovered. Recently, it was suggested that confinement into the chaperonin cage itself can significantly accelerate folding of a substrate. Performing comprehensive molecular simulations of eight proteins confined into various sizes L of chaperonin-like cage,(More)
We investigated the structural relaxation of myosin motor domain from the pre-power stroke state to the near-rigor state using molecular dynamics simulation of a coarse-grained protein model. To describe the spontaneous structural change, we propose a dual Gō-model-a variant of the Gō-like model that has two reference structures. The nucleotide dissociation(More)
Molecular motors are known to have the high efficiency of energy transformation in the presence of thermal fluctuation[1]. Motivated by the surprising fact, recent studies of thermal ratchet models[2] are showing how and when work should be extracted from non-equilibrium fluctuations[3, 4, 5, 6, 7, 8, 9, 10]. One of the important finding was brought by(More)
We investigated the structural relaxation of myosin motor domain from the pre-power stroke state to the near-rigor state using molecular dynamics simulation of a coarse-grained protein model. To describe the structural change, we propose a “dual Gō-model,” a variant of the Gō-like model that has two reference structures. The nucleotide dissociation process(More)
When a small dynamical system that is initially in contact with a heat bath is detached from this heat bath and then caused to undergo a quasi-static adiabatic process, the resulting statistical distribution of the system's energy differs from that of an equilibrium ensemble. Subsequent contact of the system with another heat bath is inevitably(More)
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(More)
X iv :0 80 2. 00 29 v1 [ qbi o. B M ] 3 1 Ja n 20 08 Structural Fluctuations of Microtubule Binding Site of KIF1A in Different Nucleotide States Ryo Kanada,1, 2, ∗ Fumiko Takagi,3, 2 and Macoto Kikuchi2, 3, 4, 5 1Department of biophysics, Kyoto University, Kyoto 606-8502, Japan 2Cybermedia Center, Osaka University, Toyonaka 560-0043, Japan 3Formation of(More)
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