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Identification of key sites controlling protein functional motions by using elastic network model combined with internal coordinates

机译:用弹性网络模型与内坐标相结合控制蛋白质功能运动的关键部位的识别

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摘要

The elastic network model (ENM) is an effective method to extract the intrinsic dynamical properties encoded in protein tertiary structures. We have proposed a new ENM-based analysis method to reveal the motion modes directly responsible for a specific protein function, in which an internal coordinate related to the specific function was introduced to construct the internal/Cartesian hybrid coordinate space. In the present work, the function-related internal coordinates combined with a linear perturbation method were applied to identify the key sites controlling specific protein functional motions. The change in the fluctuations of the internal coordinate in response to residue perturbation was calculated in the hybrid coordinate space by using the linear response theory. The residues with the large fluctuation changes were identified to be the key sites that allosterically control the specific protein function. Two proteins, i.e., human DNA polymerase beta and the chaperonin from Methanococcus maripaludis, were investigated as case studies, in which several collective and local internal coordinates were applied to identify the functionally key residues of these two studied proteins. The calculation results are consistent with the experimental observations. It is found that different collective internal coordinates lead to similar results, where the predicted functionally key sites are located at similar positions in the protein structure. While for the local internal coordinates, the predicted key sites tend to be situated at the region near to the coordinate-involving residues. Our studies provide a starting point for further exploring other function-related internal coordinates for other interesting proteins.
机译:弹性网络模型(ENM)是提取蛋白质三级结构中编码的内在动力学特性的有效方法。我们提出了一种新的基于eNM的分析方法来揭示直接负责特定蛋白质功能的运动模式,其中引入了与特定功能相关的内部坐标,以构造内部/笛卡尔混合坐标空间。在本作工作中,应用与线性扰动方法结合的功能相关的内部坐标以鉴定控制特定蛋白质功能运动的关键位点。通过使用线性响应理论在混合坐标空间中计算响应残留扰动的内部坐标波动的变化。鉴定出具有大波动变化的残留物是构成对特定蛋白质功能的关键位点。研究了两种蛋白质,即人DNA聚合酶β和来自甲基球菌的伴侣蛋白,作为案例研究,其中应用了几种集体和局部内部坐标,以鉴定这两个研究的蛋白质的功能关键残留物。计算结果与实验观察一致。发现不同的集体内部坐标导致相似的结果,其中预测的功能键位点位于蛋白质结构中的类似位置。虽然对于本地内部坐标,但是预测的关键站点往往位于靠近涉及坐标残留的地区。我们的研究提供了进一步探索其他有趣的蛋白质的其他功能相关的内坐标的起点。

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