Department of Bioscience and Biotechnology, Sejong University, 98 Kunja-Dong, Kwangjin-Ku, Seoul 143-747, Korea.
J Phys Chem B. 2010 Mar 4;114(8):2980-7. doi: 10.1021/jp909983y.
Backbone-backbone, backbone-asparagine, and serine-backbone hydrogen bonds (HBs) are the most abundant interactions at the interface of protein-protein complex. Here, we propose an angle-dependent potential energy function for these HBs constructed by the product of the radial and the angular Morse functions whose various parameters are optimized with high-level density functional theory (DFT) calculations. The new angular variables, the interatomic distance between the donor and the acceptor atoms (R(theta)) and that between the hydrogen and the base atom of the acceptor (R(phi)), are employed to define the angular Morse functions. The angular part in the new potential function is found to be comparable in the magnitude of energy values to the radial one, which is consistent with the significant angular dependence of HBs. The HB binding energies calculated with the new potential function compare well with those obtained by high-level DFT calculations with the associated squared correlation coefficients ranging from 0.82 to 0.85. This agreement indicates the suitability of the new energy functions as a potential function for HB in modeling the protein-protein interactions.
在蛋白质-蛋白质复合物的界面处，最丰富的相互作用是 backbone-backbone、backbone-asparagine 和 serine-backbone 氢键 (HBs)。在这里，我们提出了一种由径向和角度 Morse 函数的乘积构建的、适用于这些 HBs 的角度相关势能函数，其各种参数是通过高精度密度泛函理论 (DFT) 计算进行优化的。新的角度变量是供体原子和受体原子之间的原子间距离 (R(theta)) 和受体原子的氢原子和碱基原子之间的原子间距离 (R(phi))，用于定义角度 Morse 函数。新势能函数中的角度部分在能量值的大小上与径向部分相当，这与 HBs 的显著角度依赖性一致。用新势能函数计算的 HB 结合能与通过高精度 DFT 计算得到的结合能非常吻合，相关平方相关系数的范围为 0.82 到 0.85。这种一致性表明，新的能量函数作为 HB 的势能函数在建模蛋白质-蛋白质相互作用方面是合适的。
