BIOPHYSICAL THEORY AND MODELING |
Structural Change and Nucleotide Dissociation of Myosin Motor Domain: Dual Go Model Simulation
Fumiko Takagi 1* and Macoto Kikuchi 2
1 CREST JST
2 Osaka Univ.
* To whom correspondence should be addressed. E-mail: fumiko{at}cp.cmc.osaka-u.ac.jp.
Submitted on January 8, 2007
Revised on March 10, 2007
Accepted on 25 July 2007
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Abstract |
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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 Go-model,'' a variant of the Go-like model that has two reference structures. The nucleotide dissociation process is also studied by introducing a coarse-grained nucleotide in the simulation. We found that the myosin structural relaxation toward the near-rigor conformation cannot be completed before the nucleotide dissociation. Moreover, the relaxation and the dissociation occurred cooperatively when the nucleotide was tightly bound to the myosin head. The result suggested that the primary role of the nucleotide is to suppress the structural relaxation.
Key Words:
coarse-grained model, funnel picture, molecular dynamics, motor protein, strain sensor
