Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions
Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions
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DOI：
10.1016/j.polymer.2003.10.071
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发表时间：
2004-01-15
期刊：
影响因子：
4.6
通讯作者：
Doruker, P
中科院分区：
文献类型：
--
作者：
Kurkcuoglu, O;Jernigan, RL;Doruker, P
我们在蛋白质运动的正常模式分析中执行混合粗粒度方法，这使得具有低分辨率和高分辨率的不同区域的蛋白质天然构象的建模成为可能。因此，可以在高分辨率下分析超分子组合中有趣功能部分的动态，而结构的其余部分则以较差的分辨率表示，从而使系统中的节点总数保持足够低的计算可跟踪性。我们的研究结果表明，在一个大的多亚基蛋白中，通过保留结构的所有成分，无论是在更高或更低的分辨率下，都可以最好地描述特定成分的振动动力学。研究还表明，不同蛋白质和不同粗粒化水平的频率分布相似，在谱的低端，最显著的最慢运动发生的地方。(C) 2003 Elsevier Ltd.版权所有。
We perform a mixed coarse-graining approach in a normal mode analysis of protein motions, which enables the modeling of a protein's native conformation with different regions having low and high resolution. As a result, the dynamics of the interesting functional parts within a supramolecular assemblage can be analyzed at high resolution, while the remainder of the structure is represented at poorer resolution, thus keeping the total number of nodes in the system sufficiently low for computational tractability. Our results indicate that the vibrational dynamics of specific components in a large multi-subunit protein are best described by retaining all the components of the structure, whether at higher or lower resolution. It is also shown that similar frequency distributions are obtained for different proteins and at different levels of coarse-graining, at the lower end of the spectrum, where the most significant slowest motions occur. (C) 2003 Elsevier Ltd. All rights reserved.