Jiang Lin, Gao Ying, Mao Fenglou, Liu Zhijie, Lai Luhua
Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
Proteins. 2002 Feb 1;46(2):190-6. doi: 10.1002/prot.10031.
Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology. We calculate atom pair potentials for 16 pair interactions, which can reflect the importance of hydrophobic interactions and specific hydrogen-bonding interactions. The derived potentials for hydrogen-bonding interactions show a valley of favorable interactions at a distance of approximately 3 A, corresponding to that of an established hydrogen bond. For the test set of 28 protein complexes, the calculated energies have a correlation coefficient of 0.75 compared with experimental binding free energies. The performance of the method in ranking the binding energies of different protein-protein complexes shows that the energy estimation can be applied to value binding free energies for protein-protein associations.
计算蛋白质-蛋白质相互作用能对于理解蛋白质-蛋白质关联至关重要。基于平均场势方法，我们开发了一种经验方法来估计蛋白质-蛋白质相互作用的结合自由能。这种基于知识的方法已被用于从蛋白质数据库（PDB）中的非冗余训练集中推导蛋白质复合物的距离依赖性自由能，并对同源性进行了仔细处理。我们计算了16种对相互作用的原子对势，其可以反映疏水相互作用和特定氢键相互作用的重要性。推导得到的氢键相互作用势在大约3埃的距离处显示出有利相互作用的低谷，这与已确立的氢键相对应。对于28个蛋白质复合物的测试集，与实验结合自由能相比，计算得到的能量的相关系数为0.75。该方法在对不同蛋白质-蛋白质复合物的结合能进行排序方面的表现表明，能量估计可用于评估蛋白质-蛋白质关联的结合自由能。
