Duan Lili, Zhu Tong, Ji Changge, Zhang Qinggang, Zhang John Z H
School of Physics and Electronics, Shandong Normal University, Jinan 250014, China.
Phys Chem Chem Phys. 2017 Jun 14;19(23):15273-15284. doi: 10.1039/c7cp02101a.
We report a direct folding study of seven helical proteins (, Trpcage, , C34, N36, , ) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.
我们通过使用最近开发的可极化力场——有效可极化键（EPB）方法进行标准分子动力学模拟，报告了对7种螺旋蛋白（Trpcage、C34、N36等）的直接折叠研究，这些蛋白的氨基酸数量在17至53个之间。主链均方根偏差、回转半径、天然接触和天然螺旋含量与实验结果高度吻合。聚类分析也证实，这些具有最高丰度的折叠结构与这些蛋白质的相应天然结构高度一致。此外，在由均方根偏差和回转半径组成的二维空间中，7种蛋白质的自由能景观证明这些折叠结构确实是能量最低的构象。然而，当使用标准（不可极化）的AMBER力场进行相应模拟时，未观察到这些蛋白质的稳定折叠结构。基于可极化EPB力场和不可极化AMBER力场的模拟结果比较清楚地表明了极化在稳定螺旋结构折叠中的重要性。
