Nilges M, Brünger A T
Howard Hughes Medical Institute, New Haven, CT 06511.
Protein Eng. 1991 Aug;4(6):649-59. doi: 10.1093/protein/4.6.649.
A novel approach for the modeling of coiled coils through molecular dynamics is described and applied to the dimerization region of the yeast transcriptional activator GCN4. Initially, a model is created consisting of C alpha atoms only, representing an idealized coiled coil with infinite pitch. Human bias in the placing of the other atoms is reduced by an automatic building procedure using simulated annealing with simple geometric restraints. The resulting all-atom model is then allowed to relax during a short molecular dynamics run using an empirical energy function and weak restraints which reflect the coiled coil assumption. These models are then further refined using unrestrained molecular dynamics in water. In this report we test the model-building procedure on the known dimerization region of catabolyte gene activator protein (CAP), part of which forms a coiled coil, and we predict the structure of the coiled coil dimerization region (the 'leucine zipper' domain) of GCN4. Several models are built, starting from different arrangements of the C alpha atoms in the initial structures. The final structures show similar crossing angles of the coiled coil, although this was not used as a restraint in the calculation. The leucines adopt a ladder-like conformation around the 2-fold axis of the coiled coil. A number of electrostatic interactions could be identified which may contribute to the stability of the helical structure of the monomers and of the dimer.
描述了一种通过分子动力学对卷曲螺旋进行建模的新方法，并将其应用于酵母转录激活因子GCN4的二聚化区域。首先，创建一个仅由Cα原子组成的模型，代表具有无限螺距的理想化卷曲螺旋。通过使用具有简单几何约束的模拟退火自动构建程序，减少了人为在放置其他原子时的偏差。然后，使用经验能量函数和反映卷曲螺旋假设的弱约束，在短时间的分子动力学运行中使得到的全原子模型松弛。接着，在水中使用无约束分子动力学进一步优化这些模型。在本报告中，我们在已知的分解代谢物基因激活蛋白（CAP）的二聚化区域（其一部分形成卷曲螺旋）上测试了模型构建程序，并预测了GCN4卷曲螺旋二聚化区域（“亮氨酸拉链”结构域）的结构。从初始结构中Cα原子的不同排列开始构建了几个模型。最终结构显示卷曲螺旋具有相似的交叉角度，尽管在计算中未将其用作约束条件。亮氨酸在卷曲螺旋的二重轴周围呈阶梯状构象。可以识别出一些静电相互作用，这些相互作用可能有助于单体和二聚体螺旋结构的稳定性。
