Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
Structure. 2022 Apr 7;30(4):476-484.e3. doi: 10.1016/j.str.2022.02.001. Epub 2022 Feb 24.
A wide range of cellular processes requires the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The density maps produced can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low- to medium-resolution maps. Unfortunately, the models produced frequently contain atomic clashes at the protein-protein interfaces (PPIs), as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best-performing protocol, consisting of a semi-flexible simulated annealing refinement with centroid restraints on the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.
多种细胞过程都需要形成多聚体蛋白复合物。低温电子显微镜（cryo-EM）的出现使得这些蛋白组装体的结构特征得以描绘。然而，所产生的密度图仍然可能受到分辨率的限制，阻碍了以原子分辨率解析结构的过程。为了解决这个问题，可以将单体拟合到低分辨率到中分辨率的图谱中。不幸的是，所产生的模型经常在蛋白-蛋白界面（PPIs）处存在原子冲突，因为在单体拟合过程中通常不考虑分子间相互作用。在这里，我们提出了一种基于 HADDOCK2.4 的精修方法，以去除分子间冲突并优化 PPI。使用了 14 个 cryo-EM 复合物的数据集来测试八个方案。表现最好的方案，由单体中心约束的半柔性模拟退火精修组成，能够将分子间原子冲突减少 98%，而不会显著降低 cryo-EM 密度拟合的质量。
