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首页> 外文期刊>Journal of Molecular Biology >Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface.
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Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface.

机译：新的氢键网络和蛋白质-蛋白质界面上至少300倍的特异性开关的计算设计。

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摘要

The redesign of protein-protein interactions is a stringent test of our understanding of molecular recognition and specificity. Previously we engineered a modest specificity switch into the colicin E7 DNase-Im7 immunity protein complex by identifying mutations that are disruptive in the native complex, but can be compensated by mutations on the interacting partner. Here we extend the approach by systematically sampling alternate rigid body orientations to optimize the interactions in a binding mode specific manner. Using this protocol we designed a de novo hydrogen bond network at the DNase-immunity protein interface and confirmed the design with X-ray crystallographic analysis. Subsequent design of the second shell of interactions guided by insights from the crystal structure on tightly bound water molecules, conformational strain, and packing defects yielded new binding partners that exhibited specificities of at least 300-fold between the cognate and the non-cognate complexes. This multi-step approach should be applicable to the design of polar protein-protein interactions and contribute to the re-engineering of regulatory networks mediated by protein-protein interactions.
机译：蛋白质-蛋白质相互作用的重新设计是对我们对分子识别和特异性的理解的严格测试。以前，我们通过鉴定在天然复合物中具有破坏性但可以被相互作用伴侣上的突变补偿的突变，将适度的特异性转换工程改造到大肠菌素E7 DNase-Im7免疫蛋白复合物中。在这里，我们通过系统地采样交替的刚体方向来扩展该方法，从而以绑定模式特定的方式优化交互作用。使用该协议，我们在DNase-免疫蛋白界面上设计了一个从头氢键网络，并通过X射线晶体学分析证实了该设计。相互作用的第二层壳的后续设计由紧密结合的水分子的晶体结构，构象应变和堆积缺陷的洞察力指导，产生了新的结合配偶体，该配偶体在同源和非同源复合物之间显示出至少300倍的特异性。这种多步骤方法应适用于极性蛋白质-蛋白质相互作用的设计，并有助于重新构建由蛋白质-蛋白质相互作用介导的调节网络。

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