Ibragimova G T, Wade R C
European Molecular Biology Laboratory, Heidelberg, Germany.
Biophys J. 1998 Jun;74(6):2906-11. doi: 10.1016/S0006-3495(98)77997-4.
The accurate and efficient treatment of electrostatic interactions is one of the challenging problems of molecular dynamics simulation. Truncation procedures such as switching or shifting energies or forces lead to artifacts and significantly reduced accuracy. The particle mesh Ewald (PME) method is one approach to overcome these problems by providing a computationally efficient means of calculating all long-range electrostatic interactions in a periodic simulation box by use of fast Fourier transformation techniques. For the application of the PME method to the simulation of a protein with a net charge in aqueous solution, counterions are added to neutralize the system. The usual procedure is to add charge-balancing counterions close to charged residues to neutralize the protein surface. In the present article, we show that for MD simulation of a small protein of marginal stability, the YAP-WW domain, explicit modeling of 0.2 M ionic strength (in addition to the charge-balancing counterions) is necessary to maintain a stable protein structure. Without explicit ions throughout the periodic simulation box, the charge-balancing counterions on the protein surface diffuse away from the protein, resulting in destruction of the beta-sheet secondary structure of the WW domain.
静电相互作用的精确有效处理是分子动力学模拟中的难题之一。诸如切换或移动能量或力的截断程序会导致伪影并显著降低精度。粒子网格埃瓦尔德（PME）方法是一种通过使用快速傅里叶变换技术，提供一种计算效率高的方法来计算周期模拟盒中所有长程静电相互作用，从而克服这些问题的方法。为了将PME方法应用于带净电荷的蛋白质在水溶液中的模拟，需添加抗衡离子来中和系统。通常的做法是在带电荷残基附近添加电荷平衡抗衡离子以中和蛋白质表面。在本文中，我们表明，对于边缘稳定性的小蛋白质YAP-WW结构域的分子动力学模拟，除电荷平衡抗衡离子外，明确模拟0.2 M离子强度对于维持稳定的蛋白质结构是必要的。在整个周期模拟盒中没有明确的离子时，蛋白质表面的电荷平衡抗衡离子会从蛋白质扩散离开，导致WW结构域的β折叠二级结构遭到破坏。
