Systematic Detection and Characterization of Hydrogen Bonding in Proteins via Local Vibrational Modes
Systematic Detection and Characterization of Hydrogen Bonding in Proteins via Local Vibrational Modes
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DOI：
10.1021/acs.jpcb.0c11392
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发表时间：
2021-03-05
影响因子：
3.3
通讯作者：
Kraka，Elfi
中科院分区：
文献类型：
--
作者：
Verma，Niraj;Tao，Yunwen;Kraka，Elfi
我们推出了一款新软件，氢键高效检测（EDHB），它基于最近邻算法系统地检测氢键。 EDHB 对分子间和分子内氢键以及氢键网络进行分类。 EDHB 在执行速度方面优于常用的氢键检测方法。 EDHB 的一个重要附加功能是，来自先前量子化学研究的信息（即自然键轨道分析数据和二阶能量导数信息）可用于确定氢键的静电/共价特征，并计算局域模式氢键力常数作为其内在强度的定量测量。我们将 EDHB 应用于 163 种不同的蛋白质。我们发现形成不同尺寸分子内环的氢键网络是一个共同特征，对于特定的二级结构方向（例如 α 螺旋和转角）发挥着重要作用。然而，这些网络对氢键强度没有显着影响。我们全面的局部模式分析揭示了一个有趣的结果，即氢键角度是决定蛋白质中氢键强度的主导因素。 EDHB 提供广泛的应用可能性。除了蛋白质之外，EDHB 通常还可用于检测和表征蛋白质-配体相互作用、水簇和其他氢键起关键作用的系统以及分子动力学模拟中的氢键。该程序可在 https://github.com/ekraka/EDHB 免费获取。
We introduce a new software,Efficient Detection of Hydrogen Bonds(EDHB), that systematically detects hydrogen bonds based on the nearest neighbors algorithm. EDHB classifies inter- and intramolecular hydrogen bonds as well as hydrogen bond networks. EDHB outperforms commonly used hydrogen bond detection methods in terms of speed of execution. An important additional feature of EDHB is that information from preceding quantum chemical studies (i.e., natural bond orbital analysis data and second energy derivative information) can be used to determine the electrostatic/covalent character of the hydrogen bonds and to calculate local-mode hydrogen bond force constants as a quantitative measure of their intrinsic strength. We applied EDHB to a diverse set of 163 proteins. We identified hydrogen bond networks forming intramolecular rings of different sizes as a common feature playing an important role for specific secondary structure orientations such as α-helixes and turns. However, these networks do not have a significant influence on the hydrogen bond strength. Our comprehensive local-mode analysis reveals the interesting result that the hydrogen bond angle is the governing factor determining the hydrogen bond strength in a protein. EDHB offers a broad range of application possibilities. In addition to proteins, EDHB can be generally used to detect and characterize hydrogen bonds in protein–ligand interactions, water clusters, and other systems where a hydrogen bond plays a critical role, as well as during molecular dynamics simulations. The program is freely available at https://github.com/ekraka/EDHB.