Binding of small molecules to an adaptive protein-protein interface
Binding of small molecules to an adaptive protein-protein interface
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DOI：
10.1073/pnas.252756299
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发表时间：
2003-02-18
影响因子：
11.1
通讯作者：
Braisted, AC
中科院分区：
文献类型：
--
作者：
Arkin, MR;Randal, M;Braisted, AC
了解在蛋白质-蛋白质界面的结合特性已被限制到结构和突变分析的天然结合伴侣或小肽鉴定的噬菌体展示。在这里，我们提出了一个非肽基小分子的高分辨率分析，以前发现的药物化学[蒂利，J.W.，等人（1997）J. Am. 119，7589-7590]，其结合细胞因子IL-2。小分子结合到与IL-2 α受体结合的相同位点，并埋入IL-2游离结构中未见的凹槽中。结合和几个自由结构的比较表明，该网站是由两个亚网站：一个是刚性的，另一个是高度适应性，热力学数据表明，这些构象之间的能量障碍是低的。通过使用称为系链（tethering）的定点筛选方法来解剖亚位点，其中小片段通过与在这些亚位点周围引入IL-2的半胱氨酸的二硫键交换来捕获。与拴系片段的X射线结构表明，subite-binding相互作用是类似的，与原来的小分子观察到的。此外，适应性亚位点比刚性亚位点束缚了更多的化合物。因此，蛋白质-蛋白质界面的自适应性质提供了小分子结合的位点，并强调了应用基于结构的设计策略的挑战，这些策略不能准确地预测动态蛋白质表面。
Understanding binding properties at protein-protein interfaces has been limited to structural and mutational analyses of natural binding partners or small peptides identified by phage display. Here, we present a high-resolution analysis of a nonpeptidyl small molecule, previously discovered by medicinal chemistry [Tilley, J.W., et al. (1997) J. Am. Chem. Soc. 119, 7589-7590], which binds to the cytokine IL-2. The small molecule binds to the same site that binds the IL-2 a receptor and buries into a groove not seen in the free structure of IL-2. Comparison of the bound and several free structures shows this site to be composed of two subsites: one is rigid, and the other is highly adaptive, Thermodynamic data suggest the energy barriers between these conformations are low. The subsites were dissected by using a site-directed screening method called tethering, in which small fragments were captured by disulfide interchange with cysteines introduced into IL-2 around these subsites. X-ray structures with the tethered fragments show that the subsite-binding interactions are similar to those observed with the original small molecule. Moreover, the adaptive subsite tethered many more compounds than did the rigid one. Thus, the adaptive nature of a protein-protein interface provides sites for small molecules to bind and underscores the challenge of applying structure-based design strategies that cannot accurately predict a dynamic protein surface.