Hydrogen Bonds and Kinematic Mobility of Protein Molecules
Hydrogen Bonds and Kinematic Mobility of Protein Molecules
复制标题
蛋白质分子的氢键和运动迁移率
DOI：
10.1115/1.4001088
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发表时间：
2010
期刊：
影响因子：
--
通讯作者：
K. Kazerounian
中科院分区：
文献类型：
--
作者：
Z. Shahbazi;H. Ilies;K. Kazerounian
将蛋白质分子建模为运动链为开发基于多肽的分子和装置的设计、操作和制造的强大方法提供了基础。然而，这些模型具有很高的自由度(DOF)，具有相当大的计算影响。另一方面，真实的蛋白质分子在折叠过程中表现出的流动性似乎比现有运动学模型所建议的要低得多。真正蛋白质流动性较低的关键因素是在折叠过程中形成氢键。本文从机械迁移率的角度探讨了氢键在决定蛋白质结构和功能中的关键作用。回顾了现有的氢键形成的几何判据，提出了一套新的几何判据。我们表明，新的标准比其他现有的标准更好地将预测的氢键数量与生物学原理建立的氢键数量关联起来。此外，我们使用已建立的运动学流动性分析工具来评估蛋白质分子的内部流动性，并识别蛋白质的刚性和柔性部分。实验结果表明，该方法显著降低了蛋白质模型的自由度，平均降低了94%。在蛋白质折叠模拟中，DOF数量的显著减少可能会产生巨大的计算影响。
Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation, and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOFs) with considerable computational implications. On the other hand, real protein molecules appear to exhibit a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of hydrogen bonds during the folding process. In this paper, we explore the pivotal role of hydrogen bonds in determining the structure and function of the proteins from the point of view of mechanical mobility. The existing geometric criteria on the formation of hydrogen bonds are reviewed and a new set of geometric criteria is proposed. We show that the new criteria better correlate the number of predicted hydrogen bonds with those established by biological principles than other existing criteria. Furthermore, we employ established tools in kinematics mobility analysis to evaluate the internal mobility of protein molecules and to identify the rigid and flexible segments of the proteins. Our results show that the developed procedure significantly reduces the DOF of the protein models, with an average reduction of 94%. Such a dramatic reduction in the number of DOF can have enormous computational implications in protein folding simulations.
影响因子：
7.4
作者：
ONG, SW;LIU, HL;PIDGEON, C
通讯作者：
PIDGEON, C
DOI：
10.1093/protein/10.9.999
发表时间：
1997-09-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
Xu, D;Tsai, CJ;Nussinov, R
通讯作者：
Nussinov, R