Kobe Bostjan, Guncar Gregor, Buchholz Rebecca, Huber Thomas, Maco Bohumil, Cowieson Nathan, Martin Jennifer L, Marfori Mary, Forwood Jade K
School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, QLD, Australia.
Biochem Soc Trans. 2008 Dec;36(Pt 6):1438-41. doi: 10.1042/BST0361438.
Crystallography is commonly used for studying the structures of protein-protein complexes. However, a crystal structure does not define a unique protein-protein interface, and distinguishing a 'biological interface' from 'crystal contacts' is often not straightforward. A number of computational approaches exist for distinguishing them, but their error rate is high, emphasizing the need to obtain further data on the biological interface using complementary structural and functional approaches. In addition to reviewing the computational and experimental approaches for addressing this problem, we highlight two relevant examples. The first example from our laboratory involves the structure of acyl-CoA thioesterase 7, where each domain of this two-domain protein was crystallized separately, but both yielded a non-functional assembly. The structure of the full-length protein was uncovered using a combination of complementary approaches including chemical cross-linking, analytical ultracentrifugation and mutagenesis. The second example involves the platelet glycoprotein Ibalpha-thrombin complex. Two groups reported the crystal structures of this complex, but all the interacting interfaces differed between the two structures. Our computational analysis did not fully resolve the reasons for the discrepancies, but provided interesting insights into the system. This review highlights the need to complement crystallographic studies with complementary experimental and computational approaches.
晶体学常用于研究蛋白质 - 蛋白质复合物的结构。然而，晶体结构并不能定义唯一的蛋白质 - 蛋白质界面，区分“生物学界面”和“晶体接触”通常并非易事。存在多种用于区分它们的计算方法，但这些方法的错误率很高，这凸显了使用互补的结构和功能方法获取关于生物学界面的更多数据的必要性。除了回顾解决此问题的计算和实验方法外，我们还重点介绍两个相关实例。我们实验室的第一个实例涉及酰基辅酶A硫酯酶7的结构，该双结构域蛋白的每个结构域分别结晶，但两者均产生无功能的组装体。通过结合化学交联、分析超速离心和诱变等互补方法揭示了全长蛋白的结构。第二个实例涉及血小板糖蛋白Ibalpha - 凝血酶复合物。两组报告了该复合物的晶体结构，但两种结构之间所有的相互作用界面均不同。我们的计算分析并未完全解决差异的原因，但为该系统提供了有趣的见解。本综述强调了用互补的实验和计算方法补充晶体学研究的必要性。
