Cummings M D, Hart T N, Read R J
Department of Biochemistry, University of Alberta, Edmonton, Canada.
Protein Sci. 1995 May;4(5):885-99. doi: 10.1002/pro.5560040508.
The development of general strategies for the performance of docking simulations is prerequisite to the exploitation of this powerful computational method. Comprehensive strategies can only be derived from docking experiences with a diverse array of biological systems, and we have chosen the ubiquitin/diubiquitin system as a learning tool for this process. Using our multiple-start Monte Carlo docking method, we have reconstructed the known structure of diubiquitin from its two halves as well as from two copies of the uncomplexed monomer. For both of these cases, our relatively simple potential function ranked the correct solution among the lowest energy configurations. In the experiments involving the ubiquitin monomer, various structural modifications were made to compensate for the lack of flexibility and for the lack of a covalent bond in the modeled interaction. Potentially flexible regions could be identified using available biochemical and structural information. A systematic conformational search ruled out the possibility that the required covalent bond could be formed in one family of low-energy configurations, which was distant from the observed dimer configuration. A variety of analyses was performed on the low-energy dockings obtained in the experiment involving structurally modified ubiquitin. Characterization of the size and chemical nature of the interface surfaces was a powerful adjunct to our potential function, enabling us to distinguish more accurately between correct and incorrect dockings. Calculations with the structure of tetraubiquitin indicated that the dimer configuration in this molecule is much less favorable than that observed in the diubiquitin structure, for a simple monomer-monomer pair. Based on the analysis of our results, we draw conclusions regarding some of the approximations involved in our simulations, the use of diverse chemical and biochemical information in experimental design and the analysis of docking results, as well as possible modifications to our docking protocol.
开发对接模拟的通用策略是利用这种强大计算方法的前提条件。全面的策略只能从对各种生物系统的对接经验中得出，我们选择泛素/双泛素系统作为这个过程的学习工具。使用我们的多起点蒙特卡罗对接方法，我们从其两个半部分以及未复合单体的两个副本重建了双泛素的已知结构。对于这两种情况，我们相对简单的势函数在最低能量构型中将正确的解决方案列为排名靠前的。在涉及泛素单体的实验中，进行了各种结构修饰，以弥补建模相互作用中缺乏灵活性和缺乏共价键的问题。可以利用现有的生化和结构信息识别潜在的灵活区域。系统的构象搜索排除了在一个远离观察到的二聚体构型的低能量构型家族中形成所需共价键的可能性。对涉及结构修饰泛素的实验中获得的低能量对接进行了各种分析。界面表面大小和化学性质的表征是我们势函数的有力辅助手段，使我们能够更准确地区分正确和错误的对接。对四聚泛素结构的计算表明，对于一个简单的单体-单体对，该分子中的二聚体构型比在双泛素结构中观察到的构型不利得多。基于对我们结果的分析，我们得出了关于模拟中涉及的一些近似值、在实验设计和对接结果分析中使用不同化学和生化信息以及对我们对接协议可能进行的修改的结论。
