De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures
De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures
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DOI：
10.1073/pnas.1710695114
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发表时间：
2017-10-10
影响因子：
11.1
通讯作者：
DeGrado, William F.
中科院分区：
文献类型：
--
作者：
Dang, Bobo;Wu, Haifan;DeGrado, William F.
天然蛋白质的折叠通常依赖于疏水填充、金属结合或蛋白质核心中的二硫键形成。另外，可以通过结合多价交联剂来定义3D结构，这种方法已经成功地用于从大型随机序列文库中选择双环肽。相比之下，对于具有可预测和明确定义的折叠的多交联蛋白（包括自然界中没有发现的折叠）的从头计算设计，没有通用的方法。在这里，我们使用Rosetta和Tertiary Motifs （TERMs）来设计围绕多价交联剂折叠的小蛋白质。疏水交联剂通过大环约束稳定折叠，它们也形成一个小的极性核心的组成部分。设计的CovCore蛋白通过化学合成制备，并通过溶液核磁共振或x射线晶体学测定其结构。这些中等大小的蛋白质，位于传统蛋白质和小肽之间，很容易通过生物合成前体或化学合成获得。CovCore蛋白独特的三级结构和易于合成表明，它们应该为开发蛋白质-蛋白质相互作用抑制剂提供多功能模板。
The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature. Here we use Rosetta and Tertiary Motifs (TERMs) to design small proteins that fold around multivalent cross-linkers. The hydrophobic cross-linkers stabilize the fold by macrocyclic restraints, and they also form an integral part of a small apolar core. The designed CovCore proteins were prepared by chemical synthesis, and their structures were determined by solution NMR or X-ray crystallography. These mesosized proteins, lying between conventional proteins and small peptides, are easily accessible either through biosynthetic precursors or chemical synthesis. The unique tertiary structures and ease of synthesis of CovCore proteins indicate that they should provide versatile templates for developing inhibitors of protein-protein interactions.