Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure
Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure
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DOI：
10.1016/j.bpj.2009.08.019
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发表时间：
2009-11-04
影响因子：
3.4
通讯作者：
Kitao, Akio
中科院分区：
文献类型：
--
作者：
Loeffler, Hannes H.;Kitao, Akio
谷氨酰胺结合蛋白是相关ATIP结合盒转运系统的重要组成部分，负责谷氨酰胺摄入细胞。我们研究了全球运动的这种蛋白质的分子动力学模拟和主成分分析（PCA）。我们确认最主要的模式对应于蛋白质的生物学功能，即，在配体结合时的铰链型运动。关闭本身直接观察到两个独立的轨迹，其中PCA被用来阐明这种关闭反应的性质。两个中间状态被确定和详细描述。配体结合诱导铰链区从不连续的β-折叠到连续折叠的结构变化，这也增强了铰链的柔软性并改变了铰链运动的方向以实现闭合。我们还研究了PCA模式的收敛行为，发现当特征值的相关幅度很好地分离时，PCA模式收敛得相当快。
The glutamine binding protein is a vital component of the associated ATIP binding cassette transport systems responsible for the uptake of glutamine into the cell. We have investigated the global movements of this protein by molecular dynamics simulations and principal component analysis (PCA). We confirm that the most dominant mode corresponds to the biological function of the protein, i.e., a hinge-type motion upon ligand binding. The closure itself was directly observed from two independent trajectories whereby PCA was used to elucidate the nature of this closing reaction. Two intermediary states are identified and described in detail. The ligand binding induces the structural change of the hinge regions from a discontinuous beta-sheet to a continuous one, which also enhances softness of the hinge and modifies the direction of hinge motion to enable closing. We also investigated the convergence behavior of PCA modes, which were found to converge rather quickly when the associated magnitudes of the eigenvalues are well separated.