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首页> 美国卫生研究院文献>Biophysical Journal >The Influence of Interdomain Interactions on the Intradomain Motions in Yeast Phosphoglycerate Kinase: A Molecular Dynamics Study
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The Influence of Interdomain Interactions on the Intradomain Motions in Yeast Phosphoglycerate Kinase: A Molecular Dynamics Study

机译：域间相互作用对酵母磷酸甘油酸激酶中域内运动的影响：分子动力学研究。

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A 3-ns molecular dynamics simulation in explicit solvent was performed to examine the inter- and intradomain motions of the two-domain enzyme yeast phosphoglycerate kinase without the presence of substrates. To elucidate contributions from individual domains, simulations were carried out on the complete enzyme as well as on each isolated domain. The enzyme is known to undergo a hinge-bending type of motion as it cycles from an open to a closed conformation to allow the phosphoryl transfer occur. Analysis of the correlation of atomic movements during the simulations confirms hinge bending in the nanosecond timescale: the two domains of the complete enzyme exhibit rigid body motions anticorrelated with respect to each other. The correlation of the intradomain motions of both domains converges, yielding a distinct correlation map in the enzyme. In the isolated domain simulations—in which interdomain interactions cannot occur—the correlation of domain motions no longer converges and shows a very small correlation during the same simulation time. This result points to the importance of interdomain contacts in the overall dynamics of the protein. The secondary structure elements responsible for interdomain contacts are also discussed.
机译：在显式溶剂中进行了3-ns分子动力学模拟，以检查在没有底物存在的情况下双域酶酵母磷酸甘油酸激酶的域间和域内运动。为了阐明单个域的贡献，对完整的酶以及每个分离的域进行了模拟。已知该酶经历铰链弯曲类型的运动，因为它从开放构象循环到闭合构象以允许磷酸基转移发生。在模拟过程中对原子运动相关性的分析确认了纳秒级的铰链弯曲：完整酶的两个域表现出彼此反相关的刚体运动。两个域的域内运动的相关性会聚，在酶中产生不同的相关性图。在隔离域仿真中（其中不会发生域间交互作用），域运动的相关性不再收敛，并且在相同的仿真时间内显示出很小的相关性。该结果表明域间接触在蛋白质总体动力学中的重要性。还讨论了负责域间联系的二级结构元素。

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