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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 One of the important finding was brought by Magnasco[6] where he studied the temperature dependence on the(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 G¯ o-model, " a variant of the G¯ o-like model that has two reference structures. The nucleotide dissociation(More)
The chiral phase transition at finite temperature T and/or chemical potential µ is studied using the QCD-like theory with a variational approach. The form of Cornwall–Jackiw–Tomboulis effective potential is modified by the use of the Schwinger–Dyson equation for generally nonzero current quark mass. We then calculate the effective potential at finite T(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)
How molecular motors like Kinesin regulates the affinity to the rail protein in the process of ATP hydrolysis (ATP → ADP·Pi → ADP + Pi) remains to be uncovered. To understand the regulation mechanism, we investigate the structural fluctuation of KIF1A in different nucleotide states that are realized in the ATP hydrolysis process by molecular dynamics(More)
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