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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking
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Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

机译：洞察蛋白质的灵活性：蛋白质对接后正常模式与构象变化之间的关系

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摘要

Understanding protein interactions has broad implications for the mechanism of recognition, protein design, and assigning putative functions to uncharacterized proteins. Studying protein flexibility is a key component in the challenge of describing protein interactions. In this work, we characterize the observed conformational change for a set of 20 proteins that undergo large conformational change upon association ( > 2 A Cα RMSD) and ask what features of the motion are successfully reproduced by the normal modes of the system. We demonstrate that normal modes can be used to identify mobile regions and, in some proteins, to reproduce the direction of conformational change. In 35% of the proteins studied, a single low-frequency normal mode was found that describes well the direction of the observed conformational change. Finally, we find that for a set of 134 proteins from a docking benchmark that the characteristic frequencies of normal modes can be used to predict reliably the extent of observed conformational change. We discuss the implications of the results for the mechanics of protein recognition.
机译：了解蛋白质相互作用对识别机制，蛋白质设计以及将推定功能分配给未表征的蛋白质具有广泛的意义。研究蛋白质的柔韧性是描述蛋白质相互作用的挑战中的关键组成部分。在这项工作中，我们表征了一组观察到的20种蛋白质的构象变化，这些蛋白在缔合后经历了较大的构象变化（> 2 ACαRMSD），并询问系统的正常模式成功再现了运动的哪些特征。我们证明正常模式可以用于识别移动区域，并在某些蛋白质中，以重现构象变化的方向。在35％的蛋白质研究中，发现了一个低频正常模式，该模式很好地描述了所观察到的构象变化的方向。最后，我们发现，对于对接基准中的一组134种蛋白质，正常模式的特征频率可以用来可靠地预测观察到的构象变化的程度。我们讨论了结果对蛋白质识别机制的影响。

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