Cooperative Motions of Protein and Hydration Water Molecules: Molecular Dynamics Study of Scytalone Dehydratase
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- 作者：Noriaki Okimoto ; Takashi Nakamura ; Atsushi Suenaga ; Noriyuki Futatsugi ; Yoshinori Hirano ; Isamu Yamaguchi ; and Toshikazu Ebisuzaki
- 刊名：Journal of the American Chemical Society
- 出版年：2004
- 出版时间：October 13, 2004
- 年：2004
- 卷：126
- 期：40
- 页码：13132 - 13139
- 全文大小：599K
- 年卷期：v.126,no.40(October 13, 2004)
- ISSN：1520-5126
文摘
Two molecular dynamics (MD) simulations totaling 25 ns of simulation time of monomericscytalone dehydratase (SD) were performed. The enzyme has a ligand-binding pocket containing a cone-shaped 
+
barrel, and the C-terminal region covers the binding pocket. Our simulations clarified thedifference in protein dynamics and conformation between the liganded protein and the unliganded protein.The liganded protein held the ligand molecule tightly and the initial structure was maintained during thesimulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changedlargely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by openingof the C-terminal region, and the protein dynamics was connected with hydration water molecules entryinto and release from the binding pocket. In addition, the cooperative motions of the unliganded proteinand the hydration water molecules produced the path through the protein interior for ligand binding.
+ barrel, and the C-terminal region covers the binding pocket. Our simulations clarified thedifference in protein dynamics and conformation between the liganded protein and the unliganded protein.The liganded protein held the ligand molecule tightly and the initial structure was maintained during thesimulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changedlargely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by openingof the C-terminal region, and the protein dynamics was connected with hydration water molecules entryinto and release from the binding pocket. In addition, the cooperative motions of the unliganded proteinand the hydration water molecules produced the path through the protein interior for ligand binding.