Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
J Phys Chem B. 2009 Oct 22;113(42):13898-900. doi: 10.1021/jp908002n.
Molecular dynamics simulations based on the standard nonpolarizable AMBER force field and on quantum-derived polarized protein-specific charge (PPC) are performed to compute NMR scalar coupling constants across hydrogen bonds for three benchmark protein systems: ubiquitin, the GB1 domain of protein G, and the SMN Tudor domain. Direct comparison of the simulation result with experimental data gives strong evidence that intraprotein hydrogen bonds are significantly stabilized by electronic polarization, both in terms of NMR scalar coupling constants and X-ray determined geometries of hydrogen bonds. Without the polarization effect in the force field, hydrogen bonds are found to be "too loose", which leads to less stable or even unstable local structures of proteins.
基于标准非极化 AMBER 力场和源自量子力学的极化蛋白特定电荷（PPC）的分子动力学模拟，计算了三个基准蛋白系统（泛素、蛋白 G 的 GB1 结构域和 SMN Tudor 结构域）中氢键之间的 NMR 标量耦合常数。模拟结果与实验数据的直接比较有力地证明了氢键在蛋白质内部通过电子极化得到了显著稳定，这表现在 NMR 标量耦合常数和 X 射线确定的氢键几何形状上。如果力场中没有极化效应，氢键就会“过于松散”，导致蛋白质的局部结构不稳定甚至不稳定。
