Brandsdal B O, Aqvist J, Smalås A O
Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway.
Protein Sci. 2001 Aug;10(8):1584-95. doi: 10.1110/ps.940101.
The binding of P1 variants of bovine pancreatic trypsin inhibitor (BPTI) to trypsin has been investigated by means of molecular dynamics simulations. The specific interaction formed between the amino acid at the primary binding (P1) position of the binding loop of BPTI and the specificity pocket of trypsin was estimated by use of the linear interaction energy (LIE) method. Calculations for 13 of the naturally occurring amino acids at the P1 position were carried out, and the results obtained were found to correlate well with the experimental binding free energies. The LIE calculations rank the majority of the 13 variants correctly according to the experimental association energies and the mean error between calculated and experimental binding free energies is only 0.38 kcal/mole, excluding the Glu and Asp variants, which are associated with some uncertainties regarding protonation and the possible presence of counter-ions. The three-dimensional structures of the complex with three of the P1 variants (Asn, Tyr, and Ser) included in this study have not at present been solved by any experimental techniques and, therefore, were modeled on the basis of experimental data from P1 variants of similar size. Average structures were calculated from the MD simulations, from which specific interactions explaining the broad variation in association energies were identified. The present study also shows that explicit treatment of the complex water-mediated hydrogen bonding network at the protein-protein interface is of crucial importance for obtaining reliable binding free energies. The successful reproduction of relative binding energies shows that this type of methodology can be very useful as an aid in rational design and redesign of biologically active macromolecules.
通过分子动力学模拟研究了牛胰蛋白酶抑制剂（BPTI）的P1变体与胰蛋白酶的结合。利用线性相互作用能（LIE）方法估计了BPTI结合环一级结合（P1）位置的氨基酸与胰蛋白酶特异性口袋之间形成的特异性相互作用。对P1位置的13种天然存在的氨基酸进行了计算，发现所得结果与实验结合自由能有很好的相关性。LIE计算根据实验缔合能正确地对13种变体中的大多数进行了排序，计算得到的结合自由能与实验值之间的平均误差仅为0.38千卡/摩尔，但不包括Glu和Asp变体，它们在质子化和可能存在抗衡离子方面存在一些不确定性。本研究中包含的三种P1变体（Asn、Tyr和Ser）与胰蛋白酶形成的复合物的三维结构目前尚未通过任何实验技术解析，因此，是根据来自类似大小P1变体的实验数据进行建模的。从MD模拟计算出平均结构，从中确定了解释缔合能广泛变化的特异性相互作用。本研究还表明，在蛋白质-蛋白质界面明确处理复杂的水介导氢键网络对于获得可靠的结合自由能至关重要。相对结合能的成功再现表明，这种方法作为合理设计和重新设计生物活性大分子的辅助手段可能非常有用。
