Zhang Qun, Shao Dongqing, Xu Peng, Jiang Zhouting
Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
Polymers (Basel). 2021 Dec 30;14(1):123. doi: 10.3390/polym14010123.
The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples' structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions. However, the conformational changes measured by RMSD are diminished by applying the electrical field with a higher frequency. During the dipole moment analysis, we found that the magnitude and frequency of the dipole moment was directly related to the strength and frequency of the external electric field. In terms of the type of electric fields, we found that the average values of RMSD and RMSF of whole molecular protein are larger when the protein is exposed in the pulsed electric field. Concerning the typical sample 1BBL, the secondary structure analysis showed that two alpha-helix segments both transit to turns or random coils almost simultaneously when it is exposed in a pulsed electric field. Meanwhile, two segments present the different characteristic times when the transition occurs in the condition of an oscillating electric field. This study also demonstrated that the protein with fewer charged residues or more residues in forming α-helical structures display the higher conformational stability. These conclusions, achieved using MD simulations, provide a theoretical understanding of the effect of the frequency and expression form of external electric fields on the conformational changes of the all-α proteins with charged residues and the guidance for anticipative applications.
通过分子动力学模拟研究了不同频率的脉冲电场和振荡电场对全α蛋白构象性质的影响。采用均方根偏差、均方根波动、偶极矩分布和二级结构分析来评估蛋白质样品的结构特征。在模拟中，我们发现较高频率的电场会影响对二级结构转变的快速响应。然而，通过均方根偏差测量的构象变化会因施加更高频率的电场而减小。在偶极矩分析过程中，我们发现偶极矩的大小和频率与外部电场的强度和频率直接相关。就电场类型而言，我们发现当蛋白质暴露在脉冲电场中时，整个分子蛋白的均方根偏差和均方根波动的平均值更大。对于典型样品1BBL，二级结构分析表明，当它暴露在脉冲电场中时，两个α螺旋片段几乎同时转变为转角或无规卷曲。同时，在振荡电场条件下发生转变时，两个片段呈现出不同的特征时间。这项研究还表明，带电荷残基较少或形成α螺旋结构的残基较多的蛋白质表现出更高的构象稳定性。这些使用分子动力学模拟得出的结论，为理解外部电场的频率和表达形式对带有电荷残基的全α蛋白构象变化的影响提供了理论依据，并为预期应用提供了指导。
