The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains an outstanding challenge. We describe a general solution to this problem which starts with a broad exploration of the very large space of possible binding modes and interactions, and then intensifies the search in the most promising regions. We demonstrate its very broad applicability by de novo design of binding proteins to 12 diverse protein targets with very different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of four of the binder-target complexes, and all four are very close to the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvement of both. Our approach now enables targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.

中文翻译：

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仅根据靶标结构信息对蛋白质结合蛋白进行稳健的从头设计

除了目标的三维结构之外，不使用任何信息来设计结合目标蛋白质表面特定位点的蛋白质仍然是一个突出的挑战。我们描述了这个问题的一般解决方案，首先对可能的结合模式和相互作用的非常大的空间进行广泛的探索，然后在最有希望的区域中加强搜索。我们通过从头设计结合蛋白对 12 种具有非常不同形状和表面特性的不同蛋白质靶标，证明了其非常广泛的适用性。生物物理表征表明，所有小于 65 个氨基酸的结合剂都是超稳定的，并以纳摩尔至皮摩尔的亲和力结合其靶标。我们成功地解决了四种粘合剂-目标复合物的晶体结构，并且所有四个都非常接近相应的计算设计模型。近 50 万个计算设计和数十万个点突变体的实验数据为该方法的优势和局限性以及我们目前对蛋白质-蛋白质相互作用的理解提供了详细的反馈，并应指导两者的改进。我们的方法现在能够针对治疗和诊断应用的各种蛋白质上的感兴趣位点设计结合剂。