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蛋白质分子与配体的作用模式主要有直接的环区结合及铰链式结合两种方式.针对这两种不同的作用方式,我们提出采用不同的策略进行结合过程的构象研究.对于直接的环区结合模式,通过建立环区主链构象库,来实现蛋白质环区与配体的准柔性对接,并以链霉抗生物素蛋白体系为例对构象库建立的可行性进行了验证计算.对铰链结合方式,采用分步对接的方法进行计算,并具体应用于HIV蛋白酶与其小分子配体的结合过程.计算结果表明,这两种处理方法分别能较好地模拟不同类型的蛋白质与配体结合后的构象变化.
There are two main modes of interaction between protein molecule and ligand: direct loop junction and hinge junction.For these two different modes of action, we propose different strategies for the conformational study of the binding process.For the direct loop region Binding mode, the quasi-flexible docking of the protein loop region and the ligand is achieved by establishing the backbone backbone conformational library, and the feasibility of establishing the conformational library is verified by using the streptavidin system as an example. Combining with the method of step-by-step docking, and was applied to the binding process of HIV protease with its small molecule ligands.The calculated results show that these two methods can better simulate the binding of different types of proteins and ligands After the conformational changes.