Theoretical Study of Enzyme-Substrate Complex Formation by the Conformational Energy Analysis

利用高速计算机进行构象能分析，是以很好的时空分辨率“看”生物大分子动态构象的理论工具。本项目的目的是用该方法模拟蛋白酶与其底物肽形成复合物的过程，并从多个角度分析结果。我们已经发展了一种快速计算构象能函数一阶导数和二阶导数的算法，以及利用前者的能量最小化方法和Monte Carlo模拟方法。我们在上面的模拟中使用了这些方法。具体而言，我们进行了蛋白酶SGPB和其抑制剂卵类粘蛋白之间的复合物形成的模拟，以及二氢叶酸还原酶和其抑制剂之间的模拟。模拟结果表明，蛋白质中存在着两种构象柔性，即简谐构象柔性和非简谐构象柔性，它们对复合物的形成过程有着复杂的影响。因此，这两个方面的研究在一个小的球状蛋白，BPTI更详细。这两个方面的差异最直接地体现在蛋白质内部原子接触的拓扑结构上。在谐波方面，拓扑被维持，而在非谐波方面，拓扑不被维持，即，在这种构象变化的过程中，相互接触的原子对发生变化。非谐机制更容易引起局部构象变化。

The conformational energy analysis by the use of high-speed computer is a theoretical tool to "see" dynamic conformation of biopolymers by a very good space-time resolution. The purpose of this project is to carry out the simulation of the process of complex formation between proteinases and their substrate peptides by this method and to analyze the results from various points of view. We have already developed an algorithm to calculate first and second derivatives of the conformational energy function rapidly and the methods of energy minimization and Monte Carlo simulation, which use the former. We used these methods in the above simulation. To be specific, we carried out the simulation of complex formation between a proteinase SGPB and its inhibitor ovomucoid, and between dihydrofolate reductase and its inhibitor. From the results of these simulations, it is indicated that there are two types of conformational flexibilities, harmonic and anharmonic, in proteins and they have complicated influences in the processes of complex formation. Therefore these two aspects are studied in a more detail in a small globular protein, BPTI. The difference of the two aspects manifests most directly in the topology of atomic contacts in the protein interior. In the harmonic aspect, the topology is maintained, while in the anharmonic aspect it is not maintained, i.e., pairs of atoms incontact change in the process of such conformational changes. Local conformational changes can be induced more easily by the anharmonic mechanism.